Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-09-27 20:41 -0400 (Fri, 27 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4759
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4497
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4526
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4475
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 202/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbHmdb 1.10.1  (landing page)
Pierrick Roger
Snapshot Date: 2024-09-25 14:00 -0400 (Wed, 25 Sep 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_19
git_last_commit: 49eb501
git_last_commit_date: 2024-08-05 04:27:43 -0400 (Mon, 05 Aug 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    TIMEOUT    OK  

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: 1.10.1
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_1.10.1.tar.gz
StartedAt: 2024-09-26 01:22:02 -0400 (Thu, 26 Sep 2024)
EndedAt: 2024-09-26 01:25:51 -0400 (Thu, 26 Sep 2024)
EllapsedTime: 229.3 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_1.10.1.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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.10.1’
* 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 4.038  1.622  14.714
hmdbToSqlite        4.293  0.101   9.658
* 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 [2024-09-26 01:24:47.576][biodb::testContext]
biodb.INFO [2024-09-26 01:24:47.583][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:24:47.598][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2024-09-26 01:24:47.601][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:24:47.604][biodb::testContext]
biodb.INFO [2024-09-26 01:24:47.608][biodb::testThat]
biodb.INFO [2024-09-26 01:24:47.610][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2024-09-26 01:24:47.612][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:47.615][biodb::testThat]
biodb.INFO [2024-09-26 01:24:48.243][biodb::testContext]
biodb.INFO [2024-09-26 01:24:48.246][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:24:48.249][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-09-26 01:24:48.267][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:24:48.270][biodb::testContext]
biodb.INFO [2024-09-26 01:24:48.321][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-09-26 01:24:48.326][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-26 01:24:48.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:24:48.366][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-26 01:24:48.370][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-26 01:24:48.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.406][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-26 01:24:48.569][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-26 01:24:48.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.588][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[2024-09-26 01:24:48.590][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-26 01:24:48.593][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-26 01:24:48.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.613][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-26 01:24:48.634][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-26 01:24:48.637][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-26 01:24:48.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.653][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-26 01:24:48.657][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-26 01:24:48.674][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-26 01:24:48.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.695][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-26 01:24:48.698][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-26 01:24:48.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.726][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[2024-09-26 01:24:48.729][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-26 01:24:48.743][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-26 01:24:48.746][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-26 01:24:48.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.767][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-26 01:24:48.771][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-26 01:24:48.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.790][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-26 01:24:48.803][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-26 01:24:48.806][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-26 01:24:48.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.824][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-26 01:24:48.827][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-26 01:24:48.829][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-26 01:24:48.841][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-26 01:24:48.844][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-26 01:24:48.846][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-26 01:24:48.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.868][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-26 01:24:48.871][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-26 01:24:48.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.891][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-26 01:24:48.902][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-26 01:24:48.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.922][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-26 01:24:48.924][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-26 01:24:48.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.944][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-26 01:24:48.947][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-26 01:24:48.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.967][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-26 01:24:48.969][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-26 01:24:48.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:48.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:48.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:48.990][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-26 01:24:49.003][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-26 01:24:49.045][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-26 01:24:49.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:49.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:49.052][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[2024-09-26 01:24:49.073][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-26 01:24:49.076][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-26 01:24:49.079][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-26 01:24:49.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:49.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:49.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:49.108][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-26 01:24:49.290][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.357][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-26 01:24:49.380][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:24:49.385][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.407][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.411][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-26 01:24:49.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:24:49.416][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.418][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-26 01:24:49.421][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:24:49.423][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:24:49.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-26 01:24:49.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-26 01:24:49.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-26 01:24:49.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-26 01:24:49.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:24:49.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:24:49.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.497][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.499][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:24:49.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:24:49.504][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.505][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.507][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-26 01:24:49.512][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.514][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-26 01:24:49.516][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:24:49.524][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.526][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.527][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-26 01:24:49.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:24:49.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.534][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-26 01:24:49.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:24:49.538][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.541][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.543][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:24:49.543][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-26 01:24:49.543][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-26 01:24:49.543][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-26 01:24:49.543][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-26 01:24:49.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:24:49.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:24:49.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.664][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.667][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:24:49.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:24:49.679][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.681][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.684][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-26 01:24:49.700][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.705][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-26 01:24:49.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.722][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:24:49.725][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.727][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.759][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.766][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-26 01:24:49.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:24:49.785][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.787][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-26 01:24:49.790][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:24:49.792][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.806][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.808][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:24:49.825][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.830][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:24:49.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.852][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.856][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:24:49.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:24:49.860][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.863][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.877][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-26 01:24:49.881][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.884][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-26 01:24:49.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.899][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:24:49.902][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.904][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.915][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:24:49.920][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-26 01:24:49.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:24:49.937][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:49.940][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-26 01:24:49.943][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:24:49.946][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.956][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:49.959][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:49.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:24:49.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:49.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:49.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:24:49.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:50.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:50.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:24:50.018][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:50.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:24:50.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:24:50.032][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:50.035][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:50.043][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:24:50.045][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.079][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[2024-09-26 01:24:50.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.195][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[2024-09-26 01:24:50.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.284][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[2024-09-26 01:24:50.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:50.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:50.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:50.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:50.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:50.472][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-26 01:24:50.499][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-26 01:24:50.502][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-26 01:24:50.505][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-26 01:24:50.539][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-26 01:24:50.542][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-26 01:24:50.546][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-26 01:24:50.568][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-26 01:24:50.571][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-26 01:24:50.575][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-26 01:24:50.588][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-26 01:24:50.591][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-26 01:24:50.594][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-26 01:24:50.608][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-26 01:24:50.612][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-26 01:24:50.615][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-26 01:24:50.633][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-26 01:24:50.636][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-26 01:24:50.655][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-26 01:24:50.665][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-26 01:24:50.668][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-26 01:24:50.688][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-26 01:24:50.692][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-26 01:24:50.695][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-26 01:24:50.709][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-26 01:24:50.712][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-26 01:24:50.715][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-26 01:24:50.729][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-26 01:24:50.734][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-26 01:24:50.737][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-26 01:24:50.748][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-26 01:24:50.752][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-26 01:24:50.769][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-26 01:24:50.773][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-26 01:24:50.777][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-26 01:24:50.786][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-26 01:24:50.796][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-26 01:24:50.799][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-26 01:24:50.806][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-26 01:24:50.810][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-26 01:24:50.813][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-26 01:24:50.822][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-26 01:24:50.831][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-26 01:24:50.838][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-26 01:24:50.841][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-26 01:24:50.845][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-26 01:24:50.851][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-26 01:24:50.855][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-26 01:24:50.865][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-26 01:24:50.869][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-26 01:24:50.878][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-26 01:24:50.882][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-26 01:24:50.885][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-26 01:24:50.893][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-26 01:24:50.897][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-26 01:24:50.900][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-26 01:24:50.910][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-26 01:24:50.914][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-26 01:24:50.917][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-26 01:24:50.929][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-26 01:24:50.944][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-26 01:24:50.956][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-26 01:24:50.961][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-26 01:24:50.965][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-26 01:24:50.972][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-26 01:24:50.975][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-26 01:24:50.978][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-26 01:24:50.989][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-26 01:24:50.992][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-26 01:24:51.005][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-26 01:24:51.008][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-26 01:24:51.012][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-26 01:24:51.024][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-26 01:24:51.027][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-26 01:24:51.031][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-26 01:24:51.043][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-26 01:24:51.047][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-26 01:24:51.050][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-26 01:24:51.059][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-26 01:24:51.062][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-26 01:24:51.064][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-26 01:24:51.066][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-26 01:24:51.068][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-26 01:24:51.084][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-26 01:24:51.088][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-09-26 01:24:51.112][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:24:51.115][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.121][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.213][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[2024-09-26 01:24:51.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.312][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[2024-09-26 01:24:51.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:24:51.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:51.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:24:51.442][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-09-26 01:24:51.477][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:24:51.496][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:51.498][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-26 01:24:51.501][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:51.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:24:51.538][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:51.541][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-09-26 01:24:51.544][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:51.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:24:51.566][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-26 01:24:51.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:24:51.571][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:51.573][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-09-26 01:24:51.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-09-26 01:24:51.586][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-09-26 01:24:51.589][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-26 01:24:51.600][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:24:51.600][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-09-26 01:24:51.600][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-09-26 01:24:51.603][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-26 01:24:51.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:51.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:51.621][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:24:51.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:24:51.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:24:51.632][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:24:51.655][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-26 01:24:51.655][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-09-26 01:24:51.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:24:51.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:24:51.662][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-26 01:24:51.665][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:24:51.691][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-09-26 01:24:51.707][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-26 01:24:51.711][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-26 01:24:51.716][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-26 01:24:51.720][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-26 01:24:51.792][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:24:51.794][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-09-26 01:24:51.806][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:24:51.812][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:24:51.822][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:24:51.824][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:24:51.827][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-09-26 01:24:51.829][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-09-26 01:24:51.832][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-26 01:24:51.832][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-09-26 01:24:51.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:24:51.836][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:24:51.838][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-09-26 01:24:51.840][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-09-26 01:24:51.841][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:24:51.878][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:24:51.880][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:24:51.882][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:24:51.884][private$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[2024-09-26 01:24:51.886][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:24:51.887][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-09-26 01:24:51.937][biodb::testThat]
biodb.INFO [2024-09-26 01:24:51.939][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-09-26 01:24:51.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:51.948][biodb::testThat]
biodb.TRACE[2024-09-26 01:24:51.955][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-09-26 01:24:51.959][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:24:51.965][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:24:51.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:24:51.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:51.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:51.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:51.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:51.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:52.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:24:52.039][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:52.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:52.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.047][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:52.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:52.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.083][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:52.086][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:52.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.089][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.165][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:52.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:52.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.174][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.175][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.178][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.179][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.196][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:52.198][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:52.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.203][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.205][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:52.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:52.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.218][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:52.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:52.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.225][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:52.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:52.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.248][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:52.250][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:52.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.255][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:52.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:52.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.272][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:52.274][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:52.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.279][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.282][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:52.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:52.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.346][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:52.348][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:52.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.375][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:52.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:52.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.407][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:52.410][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:52.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.414][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:52.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:52.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.449][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:52.452][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:52.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.467][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:52.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:52.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.490][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:52.492][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:52.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.508][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.511][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:52.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.530][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:52.533][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:52.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.548][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:52.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:52.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.571][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:52.574][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:52.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.591][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:52.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:52.615][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:52.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.630][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:52.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:52.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.652][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:52.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:52.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.669][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.693][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:52.695][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:52.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.711][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:52.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:52.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.733][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:52.736][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:52.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.750][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.753][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:52.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:52.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.774][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:24:52.777][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:52.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.783][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.785][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:24:52.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:52.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:52.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:52.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:52.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:52.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:52.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.976][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:52.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:52.998][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:53.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.006][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:53.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:53.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:53.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:53.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.033][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:53.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:53.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.043][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:53.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:53.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:53.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:53.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:53.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:53.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:53.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:53.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:53.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:53.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:53.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.117][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:53.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:53.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.127][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:53.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.133][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:53.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.144][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:53.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:53.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.149][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:53.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:53.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:53.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.165][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:53.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:53.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:53.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:53.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.184][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:53.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.191][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:53.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:53.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.199][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:53.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:53.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:53.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:53.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:53.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:53.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:53.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:53.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:53.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:53.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:53.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:53.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:53.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:53.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.280][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:53.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:53.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.286][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:53.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:53.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.308][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:53.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:53.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:53.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:53.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:53.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:53.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:53.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.374][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:53.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:53.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.385][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:53.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:53.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.394][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:53.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:53.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:53.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:53.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.405][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:53.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:53.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.414][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:53.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:53.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:53.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:53.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.429][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:53.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:53.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:53.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.445][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:24:53.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.481][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:24:53.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:53.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:53.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:53.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.618][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.645][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:53.729][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-26 01:24:53.733][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-26 01:24:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-26 01:24:53.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-26 01:24:53.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-26 01:24:53.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-26 01:24:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-26 01:24:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-26 01:24:53.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-26 01:24:53.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.921][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:53.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:53.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:53.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:54.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.164][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:54.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:54.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:54.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.304][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.313][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:54.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.378][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.400][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.427][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.448][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.474][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.480][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.482][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:54.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.592][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.595][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.615][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:54.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.742][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.745][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.761][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.763][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:54.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.882][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.884][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.896][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.958][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:54.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:54.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:54.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:54.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:54.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:54.995][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:54.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:55.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.013][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:55.016][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:55.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.020][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:55.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:55.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:55.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.161][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:55.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:55.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.168][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:55.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.246][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:55.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:55.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:55.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.282][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:55.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:55.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.303][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:55.312][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:55.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.317][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.320][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:55.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:55.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:55.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:55.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:55.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:55.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.441][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:55.450][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:55.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.454][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.527][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.549][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.571][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.574][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.582][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.584][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:55.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.688][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.691][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.698][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:55.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.835][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.846][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.851][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.854][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.909][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.942][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.954][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.957][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.961][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:55.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:55.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:55.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:55.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.026][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.030][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.035][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.068][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:56.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:56.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.079][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:56.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.091][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:56.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:56.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.117][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:56.120][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:56.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.220][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:56.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:56.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:56.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:56.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:56.287][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:56.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.292][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:56.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.361][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.364][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.369][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.435][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.457][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.466][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.475][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.477][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.481][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.483][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:56.508][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:56.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.514][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.525][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:56.527][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:56.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.530][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.541][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.544][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:56.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.547][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.557][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:56.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:56.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.562][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.573][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:56.575][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:56.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.579][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.592][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:56.595][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:56.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.598][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.607][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.610][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:56.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.613][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.620][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:56.622][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:56.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.625][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.633][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:56.635][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:56.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.638][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.644][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:56.646][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:56.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.650][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.670][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:56.671][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:56.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.675][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.683][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.684][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:56.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.689][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.698][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:56.700][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:56.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.703][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.710][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:56.712][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:56.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.715][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.725][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:56.727][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:56.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.731][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.740][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:56.757][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:56.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.760][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.778][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:56.780][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:56.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.784][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.791][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:56.793][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:56.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.797][ef$get] fields variable is a list.
biodb.INFO [2024-09-26 01:24:56.809][biodb::testThat]
biodb.INFO [2024-09-26 01:24:56.811][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-26 01:24:56.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:56.813][biodb::testThat]
biodb.DEBUG[2024-09-26 01:24:56.844][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-26 01:24:56.856][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-26 01:24:56.863][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:56.866][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-09-26 01:24:56.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-09-26 01:24:56.871][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-26 01:24:56.891][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-09-26 01:24:56.893][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-26 01:24:56.939][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:24:56.941][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:24:56.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:24:56.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:24:56.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:24:56.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:24:56.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:24:56.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:24:56.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:24:56.967][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:56.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:56.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.975][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:56.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:56.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.982][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:56.985][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:56.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.989][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:56.993][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:56.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:56.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.001][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.002][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.005][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.006][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.013][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.015][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.017][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.019][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.026][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.030][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.038][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.055][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.068][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.084][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.086][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.088][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.097][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.099][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.101][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.103][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.109][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.110][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.113][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.123][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.125][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.127][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.137][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:57.138][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:57.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.141][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:57.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:57.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.151][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:57.152][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:57.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.154][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:57.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:57.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.169][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.174][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.184][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.188][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.198][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.200][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.202][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.218][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:57.220][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:57.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.223][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.224][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:57.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:57.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.245][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:57.246][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:57.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.249][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.250][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:57.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:57.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.257][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:24:57.259][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.261][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.263][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:24:57.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.290][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.299][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.304][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:24:57.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.310][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.315][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.322][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:24:57.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:24:57.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:24:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:24:57.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.406][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:24:57.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:24:57.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.430][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:57.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:57.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:57.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:57.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:57.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:57.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:57.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:57.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:57.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:24:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:24:57.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:57.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:57.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:24:57.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:24:57.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:24:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:24:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.681][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:24:57.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.688][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:57.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.693][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:57.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:57.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.701][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:57.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:57.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.706][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:57.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:57.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.714][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:57.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:57.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.719][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:24:57.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:24:57.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.726][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:24:57.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.753][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:24:57.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:24:57.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.791][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:57.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:57.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.797][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:57.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.827][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:57.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:24:57.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:24:57.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:24:57.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:57.876][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-26 01:24:57.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-26 01:24:57.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-26 01:24:57.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-26 01:24:57.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-26 01:24:57.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-26 01:24:57.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-26 01:24:57.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-26 01:24:57.915][biodb::testThat]
biodb.INFO [2024-09-26 01:24:57.916][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-26 01:24:57.917][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:57.918][biodb::testThat]
biodb.TRACE[2024-09-26 01:24:57.923][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.925][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:57.930][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:57.933][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-09-26 01:24:57.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:57.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:57.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.022][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-09-26 01:24:58.025][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-09-26 01:24:58.027][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-26 01:24:58.028][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-26 01:24:58.030][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.032][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.035][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:24:58.040][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.041][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:24:58.043][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:24:58.045][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:24:58.047][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:24:58.048][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:24:58.050][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:24:58.053][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-26 01:24:58.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.093][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:24:58.096][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:24:58.097][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-09-26 01:24:58.127][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.129][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.135][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.139][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-09-26 01:24:58.178][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.199][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.223][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2024-09-26 01:24:58.346][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-09-26 01:24:58.351][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-09-26 01:24:58.353][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-09-26 01:24:58.408][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.413][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.447][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:24:58.450][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.453][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:24:58.526][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:24:58.528][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:24:58.529][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:24:58.533][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:24:58.535][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:24:58.536][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-26 01:24:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.555][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.560][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:24:58.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:24:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.576][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:24:58.579][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:24:58.580][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-09-26 01:24:58.602][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.603][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.611][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.613][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-09-26 01:24:58.639][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.650][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.659][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.668][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-09-26 01:24:58.670][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-09-26 01:24:58.673][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-09-26 01:24:58.674][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-09-26 01:24:58.680][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.682][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.684][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:24:58.686][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.687][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:24:58.692][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:24:58.694][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:24:58.697][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:24:58.699][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:24:58.701][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:24:58.703][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-26 01:24:58.706][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.714][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.724][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.744][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:24:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.753][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:24:58.754][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:24:58.755][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-09-26 01:24:58.790][biodb::testThat]
biodb.INFO [2024-09-26 01:24:58.792][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-09-26 01:24:58.793][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:58.795][biodb::testThat]
biodb.TRACE[2024-09-26 01:24:58.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.870][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-09-26 01:24:58.876][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-26 01:24:58.878][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-26 01:24:58.880][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.882][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.884][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:24:58.886][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:24:58.889][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:24:58.892][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:24:58.894][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:24:58.900][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:24:58.903][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:24:58.906][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:24:58.908][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-26 01:24:58.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:58.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:24:58.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:24:58.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:58.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:24:58.938][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:24:58.940][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-09-26 01:24:58.976][biodb::testThat]
biodb.INFO [2024-09-26 01:24:58.977][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-09-26 01:24:58.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:58.985][biodb::testThat]
biodb.TRACE[2024-09-26 01:24:59.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.077][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-26 01:24:59.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-26 01:24:59.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.097][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-26 01:24:59.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-26 01:24:59.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.218][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.225][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-26 01:24:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.245][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-26 01:24:59.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-26 01:24:59.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:24:59.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-26 01:24:59.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-26 01:24:59.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:24:59.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-26 01:24:59.275][biodb::testThat]
biodb.INFO [2024-09-26 01:24:59.276][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-26 01:24:59.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:59.278][biodb::testThat]
biodb.INFO [2024-09-26 01:24:59.301][biodb::testThat]
biodb.INFO [2024-09-26 01:24:59.302][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-26 01:24:59.304][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:59.305][biodb::testThat]
biodb.INFO [2024-09-26 01:24:59.320][biodb::testThat]
biodb.INFO [2024-09-26 01:24:59.321][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-26 01:24:59.322][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:24:59.324][biodb::testThat]
biodb.DEBUG[2024-09-26 01:24:59.338][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-09-26 01:25:04.337][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-09-26 01:25:04.479][biodb::testThat]
biodb.INFO [2024-09-26 01:25:04.482][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-26 01:25:04.484][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:04.486][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:04.881][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-09-26 01:25:04.986][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:04.988][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:04.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:04.990][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:04.992][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:04.993][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:04.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:04.995][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:04.997][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:04.999][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:05.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.004][ef$get] fields variable is a list.
biodb.INFO [2024-09-26 01:25:05.006][biodb::testThat]
biodb.INFO [2024-09-26 01:25:05.007][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-09-26 01:25:05.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:05.010][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:05.014][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-09-26 01:25:05.217][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-09-26 01:25:05.236][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-09-26 01:25:05.239][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-09-26 01:25:05.241][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-09-26 01:25:05.243][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-09-26 01:25:05.259][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-09-26 01:25:05.262][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-26 01:25:05.297][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-26 01:25:05.309][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-26 01:25:05.312][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-09-26 01:25:05.317][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markera71b18a2a9efmarker".
biodb.TRACE[2024-09-26 01:25:05.330][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-09-26 01:25:05.333][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-26 01:25:05.336][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-09-26 01:25:05.349][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-09-26 01:25:05.351][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-09-26 01:25:05.354][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-26 01:25:05.357][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2024-09-26 01:25:05.391][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-09-26 01:25:05.395][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-09-26 01:25:05.397][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-09-26 01:25:05.400][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-09-26 01:25:05.476][self$addFilesToCache] Moving files to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-09-26 01:25:05.479][private$doAddFilesToCache] Destination files are [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-09-26 01:25:05.482][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-26 01:25:05.484][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-09-26 01:25:05.494][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markera71b5f42968bmarker".
biodb.TRACE[2024-09-26 01:25:05.496][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-09-26 01:25:05.499][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-09-26 01:25:05.558][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-09-26 01:25:05.584][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-26 01:25:05.586][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-26 01:25:05.589][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-26 01:25:05.608][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:05.610][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:25:05.613][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:25:05.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:05.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:05.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:05.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:05.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:05.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:05.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:05.716][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:05.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.735][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:05.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:05.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:05.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:05.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:05.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:05.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:05.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:05.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:05.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:05.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:05.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:05.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:05.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:05.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:05.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:05.958][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-09-26 01:25:05.960][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-09-26 01:25:06.055][biodb::testThat]
biodb.INFO [2024-09-26 01:25:06.058][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-09-26 01:25:06.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:06.071][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:06.114][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2024-09-26 01:25:06.117][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2024-09-26 01:25:06.130][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-26 01:25:06.134][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.138][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-09-26 01:25:06.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2024-09-26 01:25:06.160][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-26 01:25:06.172][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-26 01:25:06.175][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-26 01:25:06.179][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.191][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:25:06.194][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:25:06.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:06.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:06.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:06.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:06.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:06.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:06.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:06.254][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:06.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:06.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:06.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:06.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:06.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:06.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:06.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:06.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:06.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:06.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:06.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:06.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:06.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:06.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:06.423][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-09-26 01:25:06.439][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-09-26 01:25:06.442][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2024-09-26 01:25:06.516][biodb::testThat]
biodb.INFO [2024-09-26 01:25:06.536][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-09-26 01:25:06.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:06.554][biodb::testThat]
biodb.INFO [2024-09-26 01:25:06.680][biodb::testThat]
biodb.INFO [2024-09-26 01:25:06.683][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-09-26 01:25:06.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:06.688][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:06.704][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.708][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.721][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:25:06.725][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.727][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:25:06.741][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:25:06.743][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:25:06.746][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:25:06.748][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2024-09-26 01:25:06.792][biodb::testThat]
biodb.INFO [2024-09-26 01:25:06.803][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-09-26 01:25:06.805][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:06.808][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:06.824][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.828][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.831][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:25:06.845][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:06.847][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:25:06.851][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:25:06.864][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:25:06.866][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:25:06.869][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2024-09-26 01:25:06.911][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:06.923][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:06.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.928][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.941][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:06.944][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:06.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.949][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:06.962][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:06.965][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:06.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:06.981][ef$get] fields variable is a list.
biodb.INFO [2024-09-26 01:25:06.984][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-26 01:25:06.987][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-09-26 01:25:07.030][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-09-26 01:25:07.047][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-26 01:25:07.050][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:07.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:07.054][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:07.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:07.071][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.073][FUN] Functions in observer BiodbConfig: [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 [2024-09-26 01:25:07.093][biodb::testContext]
biodb.INFO [2024-09-26 01:25:07.098][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:25:07.100][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2024-09-26 01:25:07.103][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:25:07.118][biodb::testContext]
biodb.INFO [2024-09-26 01:25:07.138][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-09-26 01:25:07.151][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-26 01:25:07.188][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:25:07.191][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-26 01:25:07.194][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-26 01:25:07.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.216][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-26 01:25:07.234][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-26 01:25:07.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.241][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[2024-09-26 01:25:07.249][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-26 01:25:07.252][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-26 01:25:07.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.278][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-26 01:25:07.281][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-26 01:25:07.284][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-26 01:25:07.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.317][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-26 01:25:07.320][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-26 01:25:07.323][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-26 01:25:07.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.346][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-26 01:25:07.360][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-26 01:25:07.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.380][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-26 01:25:07.382][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-26 01:25:07.385][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-26 01:25:07.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.408][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-26 01:25:07.423][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-26 01:25:07.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.432][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-26 01:25:07.448][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-26 01:25:07.452][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-26 01:25:07.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.476][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-26 01:25:07.479][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-26 01:25:07.482][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-26 01:25:07.496][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-26 01:25:07.498][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-26 01:25:07.501][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-26 01:25:07.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.517][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-26 01:25:07.519][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-26 01:25:07.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.540][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-26 01:25:07.552][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-26 01:25:07.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.559][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[2024-09-26 01:25:07.563][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-26 01:25:07.566][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-26 01:25:07.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.576][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-26 01:25:07.579][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-26 01:25:07.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.590][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-26 01:25:07.593][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-26 01:25:07.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.600][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-26 01:25:07.602][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-26 01:25:07.689][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-26 01:25:07.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.698][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-26 01:25:07.707][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-26 01:25:07.709][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-26 01:25:07.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:07.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:07.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:07.718][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-26 01:25:07.799][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.801][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-26 01:25:07.802][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.803][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:07.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.811][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.813][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.817][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-26 01:25:07.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:07.820][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.822][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-26 01:25:07.825][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:07.827][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.829][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.840][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:25:07.840][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-26 01:25:07.840][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-26 01:25:07.840][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-26 01:25:07.840][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-26 01:25:07.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:07.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:07.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:07.847][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:07.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:07.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:07.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.855][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:07.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:07.860][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.862][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.865][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-26 01:25:07.869][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.871][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-26 01:25:07.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:07.875][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.877][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.878][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.881][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-26 01:25:07.884][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:07.886][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.887][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-26 01:25:07.889][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:07.890][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.891][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.893][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:25:07.893][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-26 01:25:07.893][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-26 01:25:07.893][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-26 01:25:07.893][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-26 01:25:07.894][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:07.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:07.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:07.904][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:07.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:07.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:07.908][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.910][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.911][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:07.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:07.915][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.917][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.920][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-26 01:25:07.924][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.926][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-26 01:25:07.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:07.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.937][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.939][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.941][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-26 01:25:07.943][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:07.945][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.948][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-26 01:25:07.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:07.951][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.955][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:07.957][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.958][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:07.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:07.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:07.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:07.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:07.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:07.966][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:07.971][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:07.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:07.991][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:07.993][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:07.995][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-26 01:25:08.004][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:08.006][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-26 01:25:08.008][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:08.009][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:08.011][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:08.012][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:08.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:08.022][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:08.024][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-26 01:25:08.026][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:08.027][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:08.029][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-26 01:25:08.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:08.040][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:08.043][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:08.046][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:08.052][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:08.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:08.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:08.056][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:08.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:08.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:08.060][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:08.067][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:08.069][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:08.071][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:08.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:08.149][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:08.153][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:25:08.155][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.268][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[2024-09-26 01:25:08.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.284][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[2024-09-26 01:25:08.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.312][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[2024-09-26 01:25:08.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.371][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-26 01:25:08.385][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-26 01:25:08.388][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-26 01:25:08.391][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-26 01:25:08.400][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-26 01:25:08.404][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-26 01:25:08.414][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-26 01:25:08.418][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-26 01:25:08.422][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-26 01:25:08.431][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-26 01:25:08.435][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-26 01:25:08.438][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-26 01:25:08.450][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-26 01:25:08.454][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-26 01:25:08.458][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-26 01:25:08.466][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-26 01:25:08.470][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-26 01:25:08.473][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-26 01:25:08.479][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-26 01:25:08.481][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-26 01:25:08.483][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-26 01:25:08.485][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-26 01:25:08.487][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-26 01:25:08.492][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-26 01:25:08.494][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-26 01:25:08.497][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-26 01:25:08.500][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-26 01:25:08.502][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-26 01:25:08.507][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-26 01:25:08.509][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-26 01:25:08.510][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-26 01:25:08.512][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-26 01:25:08.514][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-26 01:25:08.516][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-26 01:25:08.519][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-26 01:25:08.522][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-26 01:25:08.525][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-26 01:25:08.528][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-26 01:25:08.531][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-26 01:25:08.535][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-26 01:25:08.537][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-26 01:25:08.539][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-26 01:25:08.541][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-26 01:25:08.543][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-26 01:25:08.545][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-26 01:25:08.551][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-26 01:25:08.554][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-26 01:25:08.557][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-26 01:25:08.559][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-26 01:25:08.565][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-26 01:25:08.568][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-26 01:25:08.569][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-26 01:25:08.571][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-26 01:25:08.573][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-26 01:25:08.575][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-26 01:25:08.581][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-26 01:25:08.583][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-26 01:25:08.585][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-26 01:25:08.587][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-26 01:25:08.588][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-26 01:25:08.590][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-26 01:25:08.594][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-26 01:25:08.597][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-26 01:25:08.600][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-26 01:25:08.604][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-26 01:25:08.607][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-26 01:25:08.617][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-26 01:25:08.619][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-26 01:25:08.621][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-26 01:25:08.635][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-26 01:25:08.638][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-26 01:25:08.649][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-26 01:25:08.653][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-26 01:25:08.655][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-26 01:25:08.657][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-26 01:25:08.659][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-26 01:25:08.661][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-26 01:25:08.663][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-26 01:25:08.666][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-26 01:25:08.670][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-26 01:25:08.672][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-26 01:25:08.674][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-26 01:25:08.677][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-26 01:25:08.681][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-26 01:25:08.690][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-09-26 01:25:08.693][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:25:08.695][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.699][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.745][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[2024-09-26 01:25:08.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.759][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[2024-09-26 01:25:08.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:08.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:08.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:08.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:08.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:08.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:08.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:08.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:09.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:09.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:09.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:09.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:09.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:09.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:09.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:09.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:09.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:09.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:09.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:09.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:09.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:09.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:09.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:09.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:09.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:09.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:09.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:09.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:09.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:09.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:09.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:09.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:09.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:09.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:09.062][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-09-26 01:25:09.066][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:09.071][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:09.074][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-26 01:25:09.077][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:09.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:09.089][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:09.092][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-09-26 01:25:09.095][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:09.097][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:09.099][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-26 01:25:09.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:09.103][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:09.106][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-09-26 01:25:09.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-09-26 01:25:09.109][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-09-26 01:25:09.111][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:09.112][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:25:09.112][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-09-26 01:25:09.112][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-09-26 01:25:09.114][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-26 01:25:09.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:09.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:09.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:09.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:09.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:09.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:09.131][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-26 01:25:09.131][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-09-26 01:25:09.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:09.143][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:09.144][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:09.146][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:09.148][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-09-26 01:25:09.153][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-26 01:25:09.157][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-26 01:25:09.161][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-26 01:25:09.168][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-26 01:25:09.175][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:09.179][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-09-26 01:25:09.182][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:09.185][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:25:09.188][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:09.193][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:09.197][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-09-26 01:25:09.199][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-09-26 01:25:09.201][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-26 01:25:09.201][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-09-26 01:25:09.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:09.206][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:09.209][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-09-26 01:25:09.211][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-09-26 01:25:09.217][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:09.220][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:25:09.223][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:09.238][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:09.242][private$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[2024-09-26 01:25:09.245][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:09.258][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-09-26 01:25:09.268][biodb::testThat]
biodb.INFO [2024-09-26 01:25:09.271][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2024-09-26 01:25:09.273][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:09.275][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:09.281][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:09.285][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:09.292][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:25:09.296][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:09.306][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:25:09.309][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:25:09.311][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:25:09.312][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:25:09.314][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:25:09.327][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-09-26 01:25:09.339][biodb::testThat]
biodb.INFO [2024-09-26 01:25:09.341][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2024-09-26 01:25:09.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:09.345][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:09.349][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-09-26 01:25:09.351][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-26 01:25:09.360][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:09.364][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-09-26 01:25:09.373][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-09-26 01:25:09.377][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-26 01:25:09.380][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-09-26 01:25:09.383][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-26 01:25:09.386][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:25:09.389][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:25:09.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:09.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:09.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:09.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:09.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:09.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:09.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:09.442][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:09.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:09.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.458][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:09.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:09.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.478][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:09.481][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:09.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.493][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.496][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:09.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:09.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.538][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:09.548][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:09.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.554][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.557][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:09.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:09.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.604][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:09.607][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:09.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.611][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.641][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:09.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:09.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:09.663][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:09.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.672][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:09.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:09.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.694][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:09.697][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:09.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.730][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:09.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:09.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.768][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:09.770][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:09.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.789][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.792][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:09.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:09.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.816][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:09.818][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:09.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.832][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:09.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:09.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:09.885][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:09.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.904][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:09.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:09.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.928][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:09.943][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:09.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.949][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:09.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:09.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.967][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:09.976][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:09.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:09.983][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:09.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:09.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:10.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.016][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:10.019][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:10.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.025][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:10.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:10.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.058][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:10.061][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:10.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.077][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:10.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:10.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.095][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:10.097][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:10.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.111][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:10.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:10.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.132][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:10.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:10.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.165][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:10.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:10.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.194][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:10.197][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:10.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.216][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.219][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:10.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:10.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.240][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:10.250][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:10.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.255][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.258][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:10.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:10.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.275][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:25:10.287][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.292][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.295][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:25:10.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:10.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:10.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:10.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:10.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:10.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:10.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.397][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:10.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:10.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.419][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:10.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:10.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.449][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:10.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:10.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.490][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:10.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:10.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.513][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:10.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.537][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:10.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:10.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:10.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:10.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:10.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:10.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:10.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:10.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:10.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:10.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:10.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:10.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:10.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:10.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:10.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:10.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.711][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:10.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:10.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:10.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:10.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.754][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:10.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:10.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.771][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:10.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:10.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.792][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:10.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:10.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.853][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:10.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:10.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:10.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.894][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:10.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.921][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:10.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:10.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:10.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.960][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:10.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:10.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.980][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:10.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:10.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:10.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:10.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:11.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:11.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:11.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:11.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:11.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.152][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:11.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:11.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.171][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:11.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:11.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:11.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:11.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:11.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:11.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:11.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:11.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:11.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:11.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:11.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:11.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.387][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:11.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:11.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.412][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:11.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:11.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.439][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:11.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:11.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.458][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:11.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:11.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.478][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:11.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:11.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.498][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:11.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:11.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:11.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:11.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.538][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:25:11.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.637][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:25:11.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:11.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:11.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:11.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.860][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:11.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:11.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.880][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:11.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:11.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:11.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:11.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.920][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:11.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:11.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:11.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:11.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:11.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:11.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:11.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:11.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:11.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:11.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:12.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:12.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:12.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:12.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:12.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:12.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:12.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:12.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:12.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:12.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:12.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:12.045][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-09-26 01:25:12.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:12.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:12.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:12.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:12.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:12.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:12.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:12.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:12.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-26 01:25:12.121][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-26 01:25:12.124][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-09-26 01:25:12.126][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-09-26 01:25:12.129][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-26 01:25:12.131][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:12.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:12.135][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:12.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:12.139][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-26 01:25:12.187][biodb::testContext]
biodb.INFO [2024-09-26 01:25:12.190][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:25:12.192][biodb::testContext] Test context - Test search of entries
biodb.INFO [2024-09-26 01:25:12.202][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-26 01:25:12.204][biodb::testContext]
biodb.INFO [2024-09-26 01:25:12.230][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-09-26 01:25:12.234][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-26 01:25:12.245][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:25:12.247][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-26 01:25:12.302][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-26 01:25:12.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.338][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-26 01:25:12.341][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-26 01:25:12.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.369][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-26 01:25:12.372][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-26 01:25:12.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.400][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-26 01:25:12.415][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-26 01:25:12.418][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-26 01:25:12.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.438][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-26 01:25:12.443][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-26 01:25:12.445][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-26 01:25:12.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.465][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-26 01:25:12.479][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-26 01:25:12.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.502][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-26 01:25:12.505][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-26 01:25:12.507][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-26 01:25:12.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.527][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-26 01:25:12.543][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-26 01:25:12.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.567][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-26 01:25:12.570][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-26 01:25:12.573][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-26 01:25:12.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.594][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[2024-09-26 01:25:12.596][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-26 01:25:12.599][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-26 01:25:12.611][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-26 01:25:12.614][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-26 01:25:12.617][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-26 01:25:12.619][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-26 01:25:12.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.640][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-26 01:25:12.656][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-26 01:25:12.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.672][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-26 01:25:12.675][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-26 01:25:12.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.702][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-26 01:25:12.705][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-26 01:25:12.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-26 01:25:12.742][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-26 01:25:12.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.765][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-26 01:25:12.767][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-26 01:25:12.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.809][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-26 01:25:12.813][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-26 01:25:12.854][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-26 01:25:12.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.873][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-26 01:25:12.876][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-26 01:25:12.879][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-26 01:25:12.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:12.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:12.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:12.900][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-26 01:25:13.053][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.059][self$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[2024-09-26 01:25:13.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:13.068][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.076][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.080][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.091][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-26 01:25:13.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:13.096][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.099][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-26 01:25:13.130][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:13.133][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.135][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.137][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:25:13.137][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-26 01:25:13.137][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-26 01:25:13.137][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-26 01:25:13.137][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-26 01:25:13.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:13.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.156][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:13.171][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.176][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.189][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:13.195][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:13.197][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.212][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.215][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-26 01:25:13.220][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.238][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-26 01:25:13.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.243][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:13.246][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.257][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.260][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.264][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-26 01:25:13.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:13.270][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.272][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-26 01:25:13.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:13.287][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.291][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:25:13.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-26 01:25:13.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-26 01:25:13.293][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-26 01:25:13.293][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-26 01:25:13.301][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:13.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:13.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.319][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.332][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:13.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:13.368][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.373][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.377][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-26 01:25:13.385][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.389][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-26 01:25:13.392][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:13.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.412][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.422][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-26 01:25:13.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:13.427][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.430][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-26 01:25:13.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:13.443][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.446][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.448][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:13.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:13.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.473][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:13.489][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:13.491][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.494][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.504][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-26 01:25:13.509][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.511][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-26 01:25:13.523][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:13.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.537][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.542][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.545][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.548][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-26 01:25:13.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:13.565][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.569][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-26 01:25:13.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:13.575][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.578][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:13.604][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.607][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-26 01:25:13.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:13.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:13.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:13.637][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:13.640][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.642][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:13.645][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:13.658][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:13.661][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:13.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:25:13.667][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.726][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[2024-09-26 01:25:13.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.766][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[2024-09-26 01:25:13.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.792][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[2024-09-26 01:25:13.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.825][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[2024-09-26 01:25:13.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.906][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[2024-09-26 01:25:13.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.929][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[2024-09-26 01:25:13.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:13.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:13.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:13.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:13.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:13.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.011][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-26 01:25:14.014][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-26 01:25:14.018][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-26 01:25:14.021][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-26 01:25:14.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-26 01:25:14.030][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-26 01:25:14.033][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-26 01:25:14.036][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-26 01:25:14.040][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-26 01:25:14.043][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-26 01:25:14.056][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-26 01:25:14.060][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-26 01:25:14.063][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-26 01:25:14.066][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-26 01:25:14.070][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-26 01:25:14.073][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-26 01:25:14.082][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-26 01:25:14.085][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-26 01:25:14.088][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-26 01:25:14.091][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-26 01:25:14.094][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-26 01:25:14.097][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-26 01:25:14.099][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-26 01:25:14.102][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-26 01:25:14.106][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-26 01:25:14.109][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-26 01:25:14.112][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-26 01:25:14.114][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-26 01:25:14.116][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-26 01:25:14.119][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-26 01:25:14.123][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-26 01:25:14.127][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-26 01:25:14.130][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-26 01:25:14.132][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-26 01:25:14.135][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-26 01:25:14.138][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-26 01:25:14.141][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-26 01:25:14.144][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-26 01:25:14.148][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-26 01:25:14.155][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-26 01:25:14.158][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-26 01:25:14.160][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-26 01:25:14.171][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-26 01:25:14.174][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-26 01:25:14.176][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-26 01:25:14.177][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-26 01:25:14.179][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-26 01:25:14.181][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-26 01:25:14.185][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-26 01:25:14.188][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-26 01:25:14.191][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-26 01:25:14.193][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-26 01:25:14.195][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-26 01:25:14.197][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-26 01:25:14.200][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-26 01:25:14.202][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-26 01:25:14.205][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-26 01:25:14.210][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-26 01:25:14.213][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-26 01:25:14.215][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-26 01:25:14.217][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-26 01:25:14.218][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-26 01:25:14.220][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-26 01:25:14.225][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-26 01:25:14.227][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-26 01:25:14.230][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-26 01:25:14.233][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-26 01:25:14.237][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-26 01:25:14.240][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-26 01:25:14.243][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-26 01:25:14.245][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-26 01:25:14.247][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-26 01:25:14.249][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-26 01:25:14.252][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-26 01:25:14.254][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-26 01:25:14.255][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-26 01:25:14.257][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-26 01:25:14.259][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-26 01:25:14.261][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-26 01:25:14.265][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-26 01:25:14.268][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-26 01:25:14.270][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-26 01:25:14.272][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-26 01:25:14.277][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-26 01:25:14.279][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-09-26 01:25:14.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-26 01:25:14.282][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.285][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.341][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[2024-09-26 01:25:14.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.355][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[2024-09-26 01:25:14.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.374][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[2024-09-26 01:25:14.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-26 01:25:14.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:14.517][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-09-26 01:25:14.519][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:14.522][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:14.524][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-26 01:25:14.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:14.528][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-26 01:25:14.530][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:14.532][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-09-26 01:25:14.534][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:14.537][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-26 01:25:14.539][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-26 01:25:14.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-26 01:25:14.542][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:14.544][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-09-26 01:25:14.546][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-09-26 01:25:14.553][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-09-26 01:25:14.555][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-26 01:25:14.557][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-26 01:25:14.557][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-09-26 01:25:14.557][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-09-26 01:25:14.558][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-26 01:25:14.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:14.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:14.562][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-26 01:25:14.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-26 01:25:14.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-26 01:25:14.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-26 01:25:14.571][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-26 01:25:14.571][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-09-26 01:25:14.579][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:14.581][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:14.582][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-26 01:25:14.583][self$setPropertyValue]
biodb.DEBUG[2024-09-26 01:25:14.586][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-09-26 01:25:14.589][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-26 01:25:14.592][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-26 01:25:14.594][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-26 01:25:14.596][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-26 01:25:14.600][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:14.601][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-09-26 01:25:14.606][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:14.608][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:25:14.610][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:14.611][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:14.613][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-09-26 01:25:14.614][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-09-26 01:25:14.615][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-26 01:25:14.615][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-09-26 01:25:14.618][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-26 01:25:14.620][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-26 01:25:14.621][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-09-26 01:25:14.622][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-09-26 01:25:14.624][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-26 01:25:14.626][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:25:14.628][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:14.630][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:14.632][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-26 01:25:14.634][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-26 01:25:14.635][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-09-26 01:25:14.637][biodb::testThat]
biodb.INFO [2024-09-26 01:25:14.638][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2024-09-26 01:25:14.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-26 01:25:14.640][biodb::testThat]
biodb.DEBUG[2024-09-26 01:25:14.647][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-09-26 01:25:14.648][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-09-26 01:25:14.650][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-09-26 01:25:14.653][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:14.657][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:14.659][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:25:14.660][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:14.662][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:25:14.665][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:25:14.667][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:25:14.671][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:25:14.672][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:25:14.674][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:25:14.675][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2024-09-26 01:25:14.677][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-26 01:25:14.678][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-26 01:25:14.681][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:14.684][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-09-26 01:25:14.687][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-09-26 01:25:14.688][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-26 01:25:14.714][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-09-26 01:25:14.716][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-26 01:25:14.717][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:25:14.719][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:25:14.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:14.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:14.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:14.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:14.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:14.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:14.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:14.766][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:14.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:14.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.770][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:14.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:14.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.782][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:14.783][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:14.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.785][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.787][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:14.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:14.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.796][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:14.797][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:14.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.807][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.809][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:14.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:14.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.815][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:14.818][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:14.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.821][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.823][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:14.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:14.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.833][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:14.834][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:14.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.837][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:14.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.847][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:14.848][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:14.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.851][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.860][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:14.861][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:14.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.863][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.865][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:14.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:14.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.879][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:14.881][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:14.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.886][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:14.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:14.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.896][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:14.897][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:14.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.902][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:14.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:14.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.913][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:14.917][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:14.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.919][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:14.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:14.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.927][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:14.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:14.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.932][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:14.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:14.944][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:14.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.947][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.955][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:14.956][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:14.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.959][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:14.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:14.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.970][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:14.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:14.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.974][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.985][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:14.987][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:14.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:14.989][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:14.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:15.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.011][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:15.014][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:15.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.023][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.026][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:15.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:15.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.031][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:15.032][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:15.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.036][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.039][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:15.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:15.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.044][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:25:15.045][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.053][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.055][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:25:15.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:15.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:15.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:15.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:15.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:15.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:15.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.090][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:15.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:15.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.096][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:15.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:15.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.109][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:15.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:15.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:15.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.128][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:15.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:15.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.136][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:15.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:15.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:15.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:15.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:15.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:15.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:15.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:15.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:15.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:15.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:15.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:15.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:15.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:15.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.207][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:15.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:15.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:15.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:15.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:15.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:15.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:15.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:15.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.282][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:15.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:15.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.296][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:15.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:15.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.302][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:15.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:15.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:15.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:15.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:15.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:15.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:15.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:15.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:15.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:15.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:15.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:15.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:15.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:15.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:15.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:15.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:15.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.673][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:15.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:15.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:15.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:15.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.716][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:15.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:15.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:15.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:15.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:15.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:15.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:15.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:15.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.870][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:15.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:15.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.911][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:15.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:15.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.921][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:15.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:15.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:15.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:15.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:15.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.003][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:16.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:16.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:16.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:16.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:16.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.053][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:16.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:16.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.071][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:25:16.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.146][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:25:16.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:16.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:16.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:16.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:16.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:16.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:16.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:16.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:16.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.256][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:16.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:16.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.264][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:16.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:16.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.285][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:16.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:16.343][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-26 01:25:16.350][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.356][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:16.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:16.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.364][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:16.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:16.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.371][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:16.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:16.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:16.381][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:25:16.383][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:25:16.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:16.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:16.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:16.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:16.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:16.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:16.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:16.455][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-09-26 01:25:16.457][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-09-26 01:25:16.461][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-09-26 01:25:16.467][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-09-26 01:25:16.470][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-09-26 01:25:16.472][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-09-26 01:25:16.477][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-09-26 01:25:16.480][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-26 01:25:16.499][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-26 01:25:16.502][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-26 01:25:16.504][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-09-26 01:25:16.512][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markera71b60e80f5amarker".
biodb.TRACE[2024-09-26 01:25:16.515][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-09-26 01:25:16.518][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-26 01:25:16.521][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-09-26 01:25:16.524][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-09-26 01:25:16.545][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-09-26 01:25:16.548][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-26 01:25:16.550][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2024-09-26 01:25:16.561][private$findXmlDatabaseFile] Found files [2]: "1390a7cb3b5a6a85.tsv, hmdb_two_full_entries.xml" into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-09-26 01:25:16.563][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-09-26 01:25:16.565][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-09-26 01:25:16.567][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-09-26 01:25:16.591][self$addFilesToCache] Moving files to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-09-26 01:25:16.593][private$doAddFilesToCache] Destination files are [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-09-26 01:25:16.595][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-26 01:25:16.596][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-09-26 01:25:16.603][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markera71b23480f6amarker".
biodb.TRACE[2024-09-26 01:25:16.605][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-09-26 01:25:16.608][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-09-26 01:25:16.611][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-09-26 01:25:16.614][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-26 01:25:16.664][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-09-26 01:25:16.665][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-26 01:25:16.667][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-26 01:25:16.668][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-26 01:25:16.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:16.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:16.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:16.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:16.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:16.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:16.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:16.803][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.804][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.807][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:16.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.815][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:16.820][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:16.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.823][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.825][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:16.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.833][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:16.836][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:16.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.839][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.841][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:16.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:16.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.854][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:16.856][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:16.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.858][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:16.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:16.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.870][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:16.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.881][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:16.884][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:16.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.889][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:16.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:16.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.901][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:16.903][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:16.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.907][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.909][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:16.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.915][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:16.918][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:16.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.921][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.923][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:16.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:16.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.933][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:16.935][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:16.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.938][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:16.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:16.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.946][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:16.949][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:16.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.952][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.962][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.969][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:16.971][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:16.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.975][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:16.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.982][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:16.984][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:16.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.986][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:16.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:16.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:16.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:16.999][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.001][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.005][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.016][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.018][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.021][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.032][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.039][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.060][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:17.063][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:17.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.067][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.074][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:17.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:17.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.082][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:17.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:17.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.091][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.093][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:17.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:17.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.103][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:25:17.104][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.107][ef$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.109][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-26 01:25:17.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.136][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:17.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:17.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.145][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:17.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:17.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.151][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-26 01:25:17.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-26 01:25:17.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:17.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.171][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:17.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:17.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-26 01:25:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-26 01:25:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:17.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:17.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-26 01:25:17.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-26 01:25:17.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:17.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:17.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:17.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:17.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-26 01:25:17.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:17.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:17.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.257][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:17.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:17.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:17.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-26 01:25:17.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:17.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:17.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.282][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:17.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:17.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-26 01:25:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.313][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-26 01:25:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.332][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:17.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:17.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:17.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.348][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:17.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.355][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:17.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-26 01:25:17.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-26 01:25:17.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:17.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:17.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:17.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-26 01:25:17.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-26 01:25:17.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.461][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:17.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:17.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.472][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:17.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:17.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.479][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:17.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-26 01:25:17.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-26 01:25:17.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.538][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:17.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:17.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.549][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:17.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:17.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-26 01:25:17.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.574][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:17.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:17.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.580][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:17.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:17.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.592][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:17.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-26 01:25:17.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:17.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:17.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:17.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:17.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.617][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-26 01:25:17.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-26 01:25:17.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:25:17.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-26 01:25:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-26 01:25:17.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-26 01:25:17.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-26 01:25:17.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.915][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:17.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:17.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:17.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-26 01:25:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:17.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:17.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:17.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:17.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:18.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:18.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:18.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-26 01:25:18.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-26 01:25:18.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:18.020][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-09-26 01:25:18.021][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.027][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.036][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.042][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:18.051][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:25:18.053][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:25:18.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:18.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:18.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:18.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:18.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:18.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:18.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:18.130][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-09-26 01:25:18.132][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-09-26 01:25:18.145][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-09-26 01:25:18.150][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:18.154][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:18.157][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:25:18.161][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:18.163][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:25:18.166][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:25:18.168][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:25:18.170][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:25:18.171][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:25:18.173][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:25:18.179][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-26 01:25:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.192][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.201][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.218][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.229][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.236][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:18.245][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:25:18.247][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:25:18.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:18.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:18.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:18.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:18.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:18.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:18.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:18.274][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.306][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.331][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.342][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:18.362][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-09-26 01:25:18.363][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:25:18.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:18.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:18.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:18.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:18.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:18.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:18.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-26 01:25:18.393][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-09-26 01:25:18.396][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-09-26 01:25:18.398][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-09-26 01:25:18.411][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:18.415][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:18.420][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-26 01:25:18.423][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-26 01:25:18.425][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-26 01:25:18.429][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-26 01:25:18.431][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-26 01:25:18.433][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-26 01:25:18.435][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-26 01:25:18.438][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-26 01:25:18.439][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-26 01:25:18.446][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.480][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.490][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.502][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:18.515][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-09-26 01:25:18.518][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2024-09-26 01:25:18.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:18.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:18.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:18.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:18.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:18.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:18.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-26 01:25:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.602][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.613][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.629][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.655][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.667][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-26 01:25:18.677][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-26 01:25:18.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-26 01:25:18.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-26 01:25:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-26 01:25:18.687][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-26 01:25:18.700][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-26 01:25:18.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-26 01:25:18.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:18.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:18.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:18.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:18.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:18.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-26 01:25:18.780][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-26 01:25:18.783][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-09-26 01:25:18.789][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-09-26 01:25:18.791][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-26 01:25:18.793][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-26 01:25:18.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-26 01:25:18.806][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-26 01:25:18.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-26 01:25:18.850][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-26 01:25:18.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 19.218   1.126  44.172

Example timings

biodbHmdb.Rcheck/biodbHmdb-Ex.timings

nameusersystemelapsed
HmdbMetabolitesConn 4.038 1.62214.714
HmdbMetabolitesEntry0.7450.0261.616
hmdbToSqlite4.2930.1019.658