Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_19
git_last_commit: a7f41b2
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for biodbHmdb on kjohnson1

To the developers/maintainers of the biodbHmdb package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbHmdb
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.10.0.tar.gz
StartedAt: 2024-06-24 12:42:40 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 12:43:41 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 60.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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-arm64/Resources/library’
* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-06-24 12:43:16.089][biodb::testContext]
biodb.INFO [2024-06-24 12:43:16.094][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:16.095][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2024-06-24 12:43:16.096][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:16.097][biodb::testContext]
biodb.INFO [2024-06-24 12:43:16.099][biodb::testThat]
biodb.INFO [2024-06-24 12:43:16.099][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2024-06-24 12:43:16.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:16.101][biodb::testThat]
biodb.INFO [2024-06-24 12:43:16.227][biodb::testContext]
biodb.INFO [2024-06-24 12:43:16.228][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:16.229][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-24 12:43:16.230][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:16.231][biodb::testContext]
biodb.INFO [2024-06-24 12:43:16.243][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:16.245][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:16.255][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:16.257][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:16.258][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:16.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.261][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:16.289][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:16.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.294][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:16.295][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:16.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.298][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:16.299][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:16.300][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:16.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.303][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:16.303][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:16.304][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:16.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.308][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:16.309][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:16.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.312][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:16.312][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:16.313][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:16.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.316][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:16.317][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:16.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.320][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:16.321][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:16.322][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:16.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.325][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:16.326][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:16.327][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:16.328][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:16.329][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:16.331][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:16.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.334][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[2024-06-24 12:43:16.335][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:16.336][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:16.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.339][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:16.340][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:16.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.343][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[2024-06-24 12:43:16.343][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:16.344][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:16.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.347][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:16.348][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:16.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.351][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:16.352][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:16.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.355][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:16.356][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:16.369][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:16.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.373][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:16.374][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:16.374][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:16.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.381][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:16.417][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.432][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:43:16.434][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.435][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:16.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.437][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.438][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.439][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:16.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:16.440][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.441][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:16.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:16.443][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.444][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.444][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:16.444][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:16.444][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:16.444][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:16.444][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:16.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:16.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:16.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.458][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.459][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:16.459][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:16.460][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.461][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.462][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:16.464][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.464][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:16.465][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.466][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:16.467][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.468][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.468][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.469][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.470][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:16.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:16.472][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.473][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:16.474][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:16.475][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.476][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.477][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:16.477][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:16.477][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:16.477][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:16.477][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:16.478][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:16.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.479][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.480][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:16.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.482][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.483][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:16.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:16.486][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.486][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.487][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:16.489][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.490][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:43:16.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:16.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.493][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.494][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.495][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.496][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:16.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:16.497][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.498][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:16.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:16.500][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.500][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.501][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.502][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:16.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:16.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.507][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.508][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:16.509][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:16.510][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.510][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.511][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:16.513][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.514][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:16.515][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:16.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.517][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.518][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.520][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:16.520][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:16.521][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.522][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:16.523][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:16.524][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.525][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.526][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:16.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.528][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:16.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.530][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.531][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.532][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:16.533][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:16.533][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.534][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.539][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:16.540][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.585][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[2024-06-24 12:43:16.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.588][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[2024-06-24 12:43:16.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.607][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:16.620][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:16.621][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:16.622][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:16.624][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:16.626][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:16.627][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:16.628][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:16.629][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:16.631][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:16.632][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:16.633][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:16.634][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:16.635][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:16.637][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:16.638][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:16.639][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:16.640][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:16.641][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:16.642][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:16.644][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:16.645][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:16.647][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:16.648][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:16.649][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:16.651][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:16.652][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:16.653][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:16.654][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:16.655][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:16.657][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:16.658][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:16.659][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:16.660][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:16.661][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:16.662][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:16.663][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:16.665][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:16.666][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:16.667][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:16.668][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:16.669][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:16.670][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:16.672][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:16.673][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:16.674][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:16.675][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:16.677][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:16.678][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:16.679][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:16.680][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:16.681][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:16.683][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:16.684][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:16.685][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:16.686][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:16.687][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:16.689][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:16.690][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:16.691][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:16.692][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:16.693][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:16.694][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:16.695][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:16.696][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:16.698][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:16.699][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:16.700][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:16.701][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:16.702][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:16.703][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:16.704][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:16.706][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:16.707][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:16.709][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:16.710][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:16.711][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:16.713][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:16.714][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:16.716][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:16.717][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:16.718][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:16.720][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:16.726][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:16.728][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:16.732][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:16.733][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.735][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.745][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[2024-06-24 12:43:16.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.821][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[2024-06-24 12:43:16.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.861][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[2024-06-24 12:43:16.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:16.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:16.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:16.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:16.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:16.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:16.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:16.874][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:16.884][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:16.886][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.887][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:16.890][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.891][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-06-24 12:43:16.891][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.893][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:43:16.894][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:16.895][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.895][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-06-24 12:43:16.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-06-24 12:43:16.897][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-06-24 12:43:16.898][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:16.899][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:16.899][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-06-24 12:43:16.899][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-06-24 12:43:16.900][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:43:16.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.902][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:16.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:16.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:16.904][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:16.905][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-24 12:43:16.905][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-06-24 12:43:16.906][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:16.907][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:16.908][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:16.908][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:16.914][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-06-24 12:43:16.916][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:16.918][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:16.919][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:16.920][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:16.953][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:16.955][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-06-24 12:43:16.961][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:16.966][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:16.971][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:16.972][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:16.974][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-06-24 12:43:16.974][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-06-24 12:43:16.975][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-24 12:43:16.975][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-06-24 12:43:16.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:16.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:16.978][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-06-24 12:43:16.979][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-06-24 12:43:16.979][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:17.007][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:17.008][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:17.009][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:17.011][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:17.012][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:17.012][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-06-24 12:43:17.024][biodb::testThat]
biodb.INFO [2024-06-24 12:43:17.025][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-24 12:43:17.026][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:17.027][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:17.032][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-06-24 12:43:17.034][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:17.039][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:17.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:17.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:17.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:17.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:17.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:17.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:17.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:17.077][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.080][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.097][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.098][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.100][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.126][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.130][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.131][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.133][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.134][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.138][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.139][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.142][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.145][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.146][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.148][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.153][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.154][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.160][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.161][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.162][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.164][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.167][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.168][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.184][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.185][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.191][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.192][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.195][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.199][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.200][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.203][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.206][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:17.207][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:17.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:17.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:17.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.213][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.214][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.216][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.220][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.223][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.227][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.228][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.229][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.234][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.235][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.237][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.240][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:17.241][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:17.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.243][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:17.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:17.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.247][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:17.248][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.250][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.251][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:17.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.298][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.308][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.312][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.316][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.323][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:17.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.346][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.349][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.353][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:17.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.369][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.375][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.379][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.382][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.385][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:17.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:17.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:17.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:17.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.420][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.424][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.456][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.462][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.465][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.468][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.472][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:17.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:17.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:17.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:17.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.478][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:17.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:17.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.481][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:17.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.494][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:17.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:17.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.533][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.536][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.543][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:17.572][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-06-24 12:43:17.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:17.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:17.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:17.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:17.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:17.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:17.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.619][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.650][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.653][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.656][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:17.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.680][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.681][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.682][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:17.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:17.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.696][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.700][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.703][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.707][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.708][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.743][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.744][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.745][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:17.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.766][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.769][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.770][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.771][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.796][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.812][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.815][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.819][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.821][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:17.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.844][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:17.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:17.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.865][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.868][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.875][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.876][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.878][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:17.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:17.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.900][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.901][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.902][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.914][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.918][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.925][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.925][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.928][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:17.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.950][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.951][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.952][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.975][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.976][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:17.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:17.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:17.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:17.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.000][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.004][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.007][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.008][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.028][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.031][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.032][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.034][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.035][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.046][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.056][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.057][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.059][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.060][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.083][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.085][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.111][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.112][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.113][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.125][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.137][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.140][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.144][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.145][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.146][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.147][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.159][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.163][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.168][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.169][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.171][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.176][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.178][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.186][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.193][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.194][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.196][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.203][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.205][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.207][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.212][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.213][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.220][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.222][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.223][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.228][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.230][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.231][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.236][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:18.237][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:18.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.239][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.244][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.245][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.247][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.252][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.255][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.260][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.261][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.263][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.267][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.268][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.270][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.274][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.277][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.281][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.282][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.284][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.288][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.289][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.302][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.303][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.305][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:18.313][biodb::testThat]
biodb.INFO [2024-06-24 12:43:18.314][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-24 12:43:18.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:18.316][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:18.330][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-06-24 12:43:18.340][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-06-24 12:43:18.347][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:18.349][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-06-24 12:43:18.350][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-06-24 12:43:18.351][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:18.354][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-06-24 12:43:18.355][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:18.379][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:18.380][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:18.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:18.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:18.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:18.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:18.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:18.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:18.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:18.395][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.396][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.398][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.403][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.403][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.405][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.410][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.410][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.412][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.413][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.417][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.418][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.420][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.422][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.426][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.427][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.429][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.434][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.435][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.449][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.450][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.452][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.453][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.457][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.457][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.459][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.460][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.464][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.465][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.467][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.468][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.472][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.473][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.474][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.479][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:18.480][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:18.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.481][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:18.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:18.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.486][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.494][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.495][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.497][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.502][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.509][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.510][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.516][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.517][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.519][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.520][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.523][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.524][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.530][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:18.531][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.533][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.534][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:18.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.551][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:18.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.561][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:18.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:18.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:18.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:18.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.609][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.613][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:18.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.619][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:18.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.626][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.630][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.636][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:18.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:18.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:18.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.642][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:18.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:18.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:18.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:18.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.665][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.669][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.673][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:18.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:18.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.707][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.711][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:18.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.714][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.718][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.722][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:18.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.725][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:18.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.735][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:18.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.748][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:18.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:18.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.770][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:18.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:18.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.774][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:18.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:18.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.781][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:18.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:18.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:18.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:18.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:18.804][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-06-24 12:43:18.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-24 12:43:18.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-24 12:43:18.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-24 12:43:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-24 12:43:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-24 12:43:18.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-24 12:43:18.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:18.833][biodb::testThat]
biodb.INFO [2024-06-24 12:43:18.835][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-24 12:43:18.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:18.836][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:18.840][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.842][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.843][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:18.845][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-06-24 12:43:18.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:18.889][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-06-24 12:43:18.891][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-06-24 12:43:18.892][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-24 12:43:18.892][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-24 12:43:18.895][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:18.896][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:18.898][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:18.899][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:18.900][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:18.901][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:18.902][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:18.903][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:18.904][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:18.905][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:18.906][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-24 12:43:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:18.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:18.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:18.921][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:18.922][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:18.923][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-06-24 12:43:18.937][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.938][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.940][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:18.941][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-06-24 12:43:18.956][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.960][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:18.963][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:18.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:18.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:18.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:18.969][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[2024-06-24 12:43:19.029][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-06-24 12:43:19.031][private$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[2024-06-24 12:43:19.031][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.INFO [2024-06-24 12:43:19.046][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-06-24 12:43:19.047][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-06-24 12:43:19.049][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-06-24 12:43:19.049][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-06-24 12:43:19.051][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-06-24 12:43:19.052][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-24 12:43:19.055][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:19.057][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-24 12:43:19.058][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-06-24 12:43:19.060][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker5c6f509100d6marker".
biodb.TRACE[2024-06-24 12:43:19.061][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-06-24 12:43:19.062][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:19.064][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-06-24 12:43:19.065][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-06-24 12:43:19.066][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-06-24 12:43:19.067][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-24 12:43:19.068][private$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[2024-06-24 12:43:19.109][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-06-24 12:43:19.110][private$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[2024-06-24 12:43:19.111][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-06-24 12:43:19.112][private$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[2024-06-24 12:43:19.124][self$addFilesToCache] Moving files to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-06-24 12:43:19.125][private$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[2024-06-24 12:43:19.127][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:19.127][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-06-24 12:43:19.130][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker5c6f5fce0aecmarker".
biodb.TRACE[2024-06-24 12:43:19.131][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-06-24 12:43:19.132][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:19.132][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:19.134][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.135][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:19.157][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:19.158][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:19.159][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:19.160][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:19.161][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:19.162][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-24 12:43:19.163][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:19.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.167][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:19.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:19.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.170][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:19.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:19.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:19.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:19.177][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:19.178][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:19.179][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-06-24 12:43:19.191][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.192][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.194][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:19.195][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-06-24 12:43:19.206][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.210][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.213][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:19.219][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-06-24 12:43:19.221][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-06-24 12:43:19.222][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-06-24 12:43:19.223][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-06-24 12:43:19.224][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.226][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.227][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:19.228][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.229][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:19.230][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:19.231][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:19.232][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:19.232][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:19.233][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:19.234][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-24 12:43:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.239][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.243][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.246][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:19.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:19.249][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:19.250][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:19.251][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-06-24 12:43:19.266][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.267][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-24 12:43:19.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:19.269][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:19.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:19.309][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-06-24 12:43:19.310][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-24 12:43:19.311][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-24 12:43:19.312][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.314][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.316][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:19.317][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:19.319][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:19.320][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:19.321][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:19.322][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:19.323][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:19.324][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:19.325][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-24 12:43:19.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:19.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:19.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:19.340][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:19.341][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-06-24 12:43:19.356][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.357][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-24 12:43:19.358][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:19.358][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:19.379][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:19.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:19.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.440][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:19.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:19.451][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:19.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:19.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:19.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:19.462][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.463][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-24 12:43:19.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:19.464][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.473][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.474][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-24 12:43:19.475][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:19.476][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.484][biodb::testThat]
biodb.INFO [2024-06-24 12:43:19.485][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-24 12:43:19.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:19.487][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:19.490][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-06-24 12:43:29.704][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-06-24 12:43:29.891][biodb::testThat]
biodb.INFO [2024-06-24 12:43:29.892][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-24 12:43:29.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:29.894][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:30.925][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-06-24 12:43:31.105][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:31.106][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:31.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.108][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.109][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:31.110][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:31.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.112][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:31.113][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:31.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.115][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:31.116][biodb::testThat]
biodb.INFO [2024-06-24 12:43:31.117][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-24 12:43:31.118][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:31.119][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:31.121][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-24 12:43:31.179][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-06-24 12:43:31.181][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-06-24 12:43:31.183][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-06-24 12:43:31.184][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-06-24 12:43:31.185][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-06-24 12:43:31.186][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-06-24 12:43:31.187][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-24 12:43:31.189][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:31.190][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-24 12:43:31.191][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-06-24 12:43:31.193][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker5c6f2d9583f4marker".
biodb.TRACE[2024-06-24 12:43:31.194][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-06-24 12:43:31.195][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:31.196][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-06-24 12:43:31.198][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-06-24 12:43:31.210][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-06-24 12:43:31.212][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-24 12:43:31.213][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2024-06-24 12:43:31.218][private$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[2024-06-24 12:43:31.220][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-06-24 12:43:31.221][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-06-24 12:43:31.222][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-06-24 12:43:31.234][self$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[2024-06-24 12:43:31.235][private$doAddFilesToCache] Destination files are [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-06-24 12:43:31.236][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-24 12:43:31.237][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-06-24 12:43:31.239][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker5c6f330a1f8dmarker".
biodb.TRACE[2024-06-24 12:43:31.240][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-06-24 12:43:31.241][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-06-24 12:43:31.257][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-24 12:43:31.298][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:31.299][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:31.300][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:31.302][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.303][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:31.304][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:31.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:31.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.315][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.TRACE[2024-06-24 12:43:31.317][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.321][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:31.347][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-24 12:43:31.348][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-24 12:43:31.367][biodb::testThat]
biodb.INFO [2024-06-24 12:43:31.368][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-24 12:43:31.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:31.370][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:31.380][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2024-06-24 12:43:31.381][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2024-06-24 12:43:31.382][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-06-24 12:43:31.384][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.386][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-06-24 12:43:31.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2024-06-24 12:43:31.389][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:31.390][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:31.391][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:31.392][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.394][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:31.395][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:31.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:31.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.406][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.TRACE[2024-06-24 12:43:31.407][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.418][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:31.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:31.443][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-24 12:43:31.443][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-24 12:43:31.444][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2024-06-24 12:43:31.457][biodb::testThat]
biodb.INFO [2024-06-24 12:43:31.458][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-24 12:43:31.459][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:31.460][biodb::testThat]
biodb.INFO [2024-06-24 12:43:31.482][biodb::testThat]
biodb.INFO [2024-06-24 12:43:31.483][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-24 12:43:31.484][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:31.485][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:31.487][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.488][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.489][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:31.491][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.491][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:31.493][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:31.494][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:31.494][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:31.495][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2024-06-24 12:43:31.503][biodb::testThat]
biodb.INFO [2024-06-24 12:43:31.504][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-24 12:43:31.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:31.506][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:31.508][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.509][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.510][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:31.512][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:31.512][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:31.513][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:31.514][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:31.515][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:31.516][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2024-06-24 12:43:31.532][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:31.533][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:31.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.535][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.536][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:31.537][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:31.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:31.539][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:31.540][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:31.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:31.541][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:31.542][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:31.543][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-06-24 12:43:31.551][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-06-24 12:43:31.552][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:31.553][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.554][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.556][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:31.561][biodb::testContext]
biodb.INFO [2024-06-24 12:43:31.562][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:31.563][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2024-06-24 12:43:31.564][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:31.565][biodb::testContext]
biodb.INFO [2024-06-24 12:43:31.570][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:31.571][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:31.576][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:31.577][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:31.578][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:31.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.581][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:31.582][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:31.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.585][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:31.585][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:31.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.588][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:31.589][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:31.590][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:31.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.594][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:31.595][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:31.596][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:31.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.599][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:31.600][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:31.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.603][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:31.604][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:31.605][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:31.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.608][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:31.609][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:31.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.613][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:31.613][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:31.614][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:31.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.617][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:31.618][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:31.619][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:31.620][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:31.621][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:31.622][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:31.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.626][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:31.627][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:31.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.630][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:31.631][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:31.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.642][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:31.643][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:31.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.646][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:31.647][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:31.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.649][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[2024-06-24 12:43:31.650][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:31.651][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:31.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.654][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:31.655][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:31.672][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:31.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.677][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:31.678][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:31.680][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:31.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.684][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:31.685][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.686][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:43:31.687][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:31.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.690][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.690][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.691][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:31.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:31.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.693][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:31.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:31.694][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.695][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.695][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:31.695][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:31.695][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:31.695][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:31.695][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:31.697][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:31.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.699][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:31.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.701][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.702][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.702][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.703][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:31.704][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:31.705][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.706][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.707][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:31.708][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.710][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:31.710][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:31.712][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.712][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.713][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.714][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:31.714][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:31.716][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.717][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:31.718][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:31.719][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.720][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.721][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:31.721][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:31.721][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:31.721][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:31.721][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:31.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:31.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:31.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.727][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.728][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.729][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:31.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:31.730][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.731][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.732][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:31.734][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.735][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:43:31.736][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:31.738][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.738][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.740][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.740][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.741][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:31.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:31.742][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.742][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:31.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:31.743][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.743][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.744][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.744][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:31.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.752][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:31.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.755][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.755][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.756][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:31.756][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:31.756][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.756][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.757][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:31.758][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.758][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:31.759][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.759][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:31.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.760][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.761][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.761][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:31.762][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:31.763][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.763][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:31.764][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:31.765][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.765][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.766][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:31.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:31.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.768][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.768][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.769][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:31.769][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:31.769][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.769][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.770][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:31.770][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.778][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[2024-06-24 12:43:31.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.792][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[2024-06-24 12:43:31.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.807][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[2024-06-24 12:43:31.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.821][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[2024-06-24 12:43:31.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.824][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:31.825][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:31.826][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:31.827][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:31.828][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:31.830][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:31.831][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:31.832][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:31.833][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:31.835][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:31.836][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:31.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:31.838][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:31.839][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:31.840][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:31.841][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:31.842][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:31.842][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:31.843][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:31.843][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:31.844][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:31.844][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:31.845][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:31.845][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:31.846][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:31.846][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:31.847][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:31.847][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:31.848][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:31.848][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:31.849][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:31.849][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:31.850][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:31.850][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:31.851][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:31.851][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:31.852][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:31.852][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:31.853][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:31.854][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:31.854][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:31.855][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:31.855][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:31.856][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:31.856][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:31.857][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:31.857][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:31.858][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:31.859][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:31.859][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:31.859][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:31.860][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:31.861][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:31.861][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:31.862][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:31.862][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:31.863][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:31.863][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:31.863][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:31.864][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:31.864][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:31.865][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:31.867][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:31.874][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:31.876][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:31.877][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:31.878][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:31.878][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:31.879][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:31.879][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:31.880][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:31.880][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:31.881][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:31.881][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:31.882][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:31.883][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:31.883][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:31.884][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:31.884][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:31.885][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:31.885][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:31.886][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:31.887][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:31.887][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:31.888][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:31.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:31.889][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.890][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.929][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[2024-06-24 12:43:31.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:31.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:31.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:31.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:31.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:31.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:31.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:31.964][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:31.966][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:31.968][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.969][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.969][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.969][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:31.970][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.970][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-06-24 12:43:31.970][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.971][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.971][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:43:31.972][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:31.972][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-06-24 12:43:31.973][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-06-24 12:43:31.974][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:31.974][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:31.974][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-06-24 12:43:31.974][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-06-24 12:43:31.974][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:43:31.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:31.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:31.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:31.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:31.977][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-24 12:43:31.977][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-06-24 12:43:31.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:31.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:31.978][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:31.979][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:31.980][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-06-24 12:43:31.981][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:31.981][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:31.983][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:31.985][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:31.988][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:31.989][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-06-24 12:43:31.990][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:31.991][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:31.992][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:31.993][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:31.994][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-06-24 12:43:31.994][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-06-24 12:43:31.995][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-24 12:43:31.995][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-06-24 12:43:31.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:31.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:31.996][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-06-24 12:43:31.996][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-06-24 12:43:31.997][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:31.997][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:31.998][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:31.999][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:31.999][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:32.000][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:32.000][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-06-24 12:43:32.001][biodb::testThat]
biodb.INFO [2024-06-24 12:43:32.002][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2024-06-24 12:43:32.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:32.010][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:32.015][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.017][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.018][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:32.019][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.020][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:32.022][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:32.022][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:32.023][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:32.023][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:32.025][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-06-24 12:43:32.028][biodb::testThat]
biodb.INFO [2024-06-24 12:43:32.029][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2024-06-24 12:43:32.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:32.030][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:32.031][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-06-24 12:43:32.031][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-06-24 12:43:32.032][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.033][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-06-24 12:43:32.034][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-06-24 12:43:32.034][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:32.035][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-06-24 12:43:32.036][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:32.036][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:32.037][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:32.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:32.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.044][FUN] Functions in observer BiodbConfig: [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[2024-06-24 12:43:32.046][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.047][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.049][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.052][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.053][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.054][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.056][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.056][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.057][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.058][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.059][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.060][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.061][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.061][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.064][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.065][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.067][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.070][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.070][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.071][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.073][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.074][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.074][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.075][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.085][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.087][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.095][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.096][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.098][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.099][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.102][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.103][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.106][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.109][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.110][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.112][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.114][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.115][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.118][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.118][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.123][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.125][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.126][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.128][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.129][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.130][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.131][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.132][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.132][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.133][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.134][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:32.135][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:32.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.143][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.151][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.156][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.157][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.158][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.182][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.186][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.207][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.210][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.212][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.247][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.250][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.272][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.279][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.282][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.286][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.289][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.296][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.300][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:32.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.319][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:32.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.340][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:32.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:32.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.342][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:32.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:32.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.345][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:32.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:32.364][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-06-24 12:43:32.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:32.382][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:32.383][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-06-24 12:43:32.383][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-06-24 12:43:32.384][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:32.384][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.385][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.385][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:32.388][biodb::testContext]
biodb.INFO [2024-06-24 12:43:32.389][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:32.396][biodb::testContext] Test context - Test search of entries
biodb.INFO [2024-06-24 12:43:32.397][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:32.398][biodb::testContext]
biodb.INFO [2024-06-24 12:43:32.403][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:32.405][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:32.410][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:32.411][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:32.412][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:32.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.415][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:32.416][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:32.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.419][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:32.419][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:32.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.421][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:32.421][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:32.422][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:32.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.423][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:32.423][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:32.424][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:32.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.425][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:32.425][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:32.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.427][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:32.427][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:32.427][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:32.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.428][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[2024-06-24 12:43:32.429][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:32.429][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:32.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.430][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:32.431][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:32.431][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:32.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.432][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:32.432][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:32.433][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:32.433][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:32.433][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:32.434][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:32.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.435][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:32.436][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:32.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.437][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:32.437][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:32.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.439][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:32.439][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:32.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.441][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:32.441][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:32.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.443][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:32.443][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:32.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.445][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:32.445][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:32.457][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:32.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.461][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:32.462][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:32.463][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:32.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.466][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:32.468][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.476][self$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[2024-06-24 12:43:32.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.480][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:32.481][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.481][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.482][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.482][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:32.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:32.483][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.484][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:32.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:32.484][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:32.485][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:32.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.486][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:32.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.487][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.488][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.488][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:32.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:32.489][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.489][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.490][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:32.491][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.493][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:32.494][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:32.496][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.497][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.498][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.499][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:32.500][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:32.501][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.502][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:32.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:32.504][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.504][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.505][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:32.505][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:32.505][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:32.505][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:32.505][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:32.506][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:32.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.508][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.509][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:32.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.512][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:32.513][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:32.514][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.514][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.515][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:32.516][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.516][self$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[2024-06-24 12:43:32.517][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.517][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:32.517][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.518][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.519][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:32.519][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:32.519][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.520][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:32.520][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:32.521][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.521][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.522][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.522][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:32.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:32.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.525][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:32.525][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:32.526][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.526][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.526][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:32.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.528][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:32.528][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.529][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:32.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.530][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.531][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:32.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:32.531][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.532][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:32.532][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:32.532][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.532][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.538][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.539][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:32.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:32.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.542][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.542][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:32.543][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:32.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.543][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.544][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:32.544][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.550][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[2024-06-24 12:43:32.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.559][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[2024-06-24 12:43:32.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.576][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:32.577][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:32.577][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:32.578][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:32.579][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:32.581][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:32.582][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:32.591][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:32.593][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:32.594][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:32.595][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:32.595][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:32.596][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:32.596][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:32.597][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:32.597][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:32.598][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:32.598][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:32.599][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:32.599][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:32.600][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:32.601][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:32.601][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:32.602][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:32.603][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:32.603][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:32.604][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:32.605][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:32.605][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:32.606][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:32.606][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:32.607][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:32.608][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:32.608][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:32.609][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:32.609][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:32.610][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:32.610][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:32.611][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:32.611][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:32.612][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:32.612][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:32.613][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:32.613][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:32.614][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:32.614][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:32.615][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:32.615][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:32.616][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:32.616][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:32.617][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:32.617][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:32.618][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:32.618][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:32.619][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:32.619][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:32.620][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:32.620][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:32.620][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:32.621][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:32.622][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:32.622][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:32.623][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:32.624][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:32.624][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:32.625][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:32.626][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:32.627][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:32.628][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:32.628][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:32.629][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:32.630][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:32.630][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:32.631][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:32.631][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:32.632][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:32.632][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:32.639][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:32.641][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:32.642][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:32.643][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:32.643][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:32.644][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:32.644][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:32.645][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:32.646][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:32.646][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.647][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.649][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[2024-06-24 12:43:32.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.696][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[2024-06-24 12:43:32.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:32.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:32.715][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:32.716][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:32.717][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.717][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.718][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.719][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:32.719][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.720][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-06-24 12:43:32.720][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.721][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.721][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:43:32.722][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:32.723][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.724][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-06-24 12:43:32.724][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-06-24 12:43:32.725][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:32.726][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:32.726][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-06-24 12:43:32.726][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-06-24 12:43:32.726][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:43:32.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.728][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:32.729][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:32.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:32.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:32.731][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-24 12:43:32.731][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-06-24 12:43:32.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:32.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:32.732][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:32.733][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:32.735][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-06-24 12:43:32.736][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:32.738][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:32.739][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:32.740][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:32.744][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:32.745][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-06-24 12:43:32.746][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:32.748][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:32.749][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:32.750][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:32.751][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-06-24 12:43:32.752][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-06-24 12:43:32.753][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-24 12:43:32.753][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-06-24 12:43:32.754][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:32.754][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:32.755][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-06-24 12:43:32.756][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-06-24 12:43:32.757][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-24 12:43:32.757][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:32.758][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:32.759][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:32.760][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-24 12:43:32.762][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:32.763][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-06-24 12:43:32.764][biodb::testThat]
biodb.INFO [2024-06-24 12:43:32.765][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2024-06-24 12:43:32.765][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:32.766][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:32.767][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-06-24 12:43:32.768][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-06-24 12:43:32.769][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-06-24 12:43:32.770][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.771][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.772][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:32.772][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.773][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:32.778][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:32.779][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:32.780][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:32.780][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:32.781][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:32.782][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2024-06-24 12:43:32.784][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-06-24 12:43:32.785][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-06-24 12:43:32.786][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:32.788][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-06-24 12:43:32.789][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-06-24 12:43:32.790][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:32.792][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-06-24 12:43:32.794][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:32.795][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:32.796][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:32.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:32.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:32.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:32.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:32.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:32.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:32.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:32.809][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.809][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.811][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.814][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.815][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.816][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.817][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:32.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.821][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.821][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.823][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.824][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.827][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.828][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.830][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.831][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.835][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.836][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:32.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.844][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.845][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:32.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.852][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.855][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.856][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:32.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.859][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.860][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.862][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:32.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.866][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.867][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:32.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.882][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.883][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.885][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.886][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:32.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.890][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.890][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.892][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.893][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:32.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:32.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.896][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.898][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.900][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:32.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:32.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.906][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.907][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:32.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.913][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.914][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.916][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:32.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.920][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.923][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:32.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:32.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.928][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.929][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.930][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.932][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:32.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:32.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.935][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.936][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.938][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:32.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:32.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.942][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:32.943][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.945][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.946][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:32.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:32.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.964][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.968][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:32.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.988][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.994][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:32.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:32.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.028][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.031][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.035][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.038][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.044][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.051][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.054][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.058][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.061][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.105][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.108][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.111][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.135][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.138][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.141][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.151][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.155][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.158][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.161][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.165][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:33.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.178][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:33.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.200][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.204][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.211][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.223][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.246][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-06-24 12:43:33.246][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.250][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.253][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.256][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.260][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:33.260][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:33.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:33.272][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-06-24 12:43:33.273][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-06-24 12:43:33.275][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.276][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-06-24 12:43:33.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-06-24 12:43:33.279][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:33.280][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-06-24 12:43:33.281][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:33.282][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:33.284][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-24 12:43:33.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:33.309][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.312][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.316][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.317][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.319][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.320][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.324][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.325][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.327][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.328][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.331][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.332][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.334][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.336][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.342][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.346][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.347][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.353][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.354][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.357][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.360][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.361][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.363][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.364][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.368][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.369][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.370][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.375][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.376][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.377][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.379][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.383][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.384][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.385][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.390][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.391][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.392][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.407][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.408][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.410][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.415][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.416][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.417][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.422][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.423][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.425][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.429][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.430][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.432][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.433][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.437][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.438][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.442][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.446][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:33.446][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-24 12:43:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.463][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.467][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.470][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.474][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.477][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.481][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-24 12:43:33.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:33.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-24 12:43:33.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-24 12:43:33.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-24 12:43:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.548][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.551][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:33.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:33.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:33.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:33.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.590][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.594][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.597][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:33.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:33.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.640][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:33.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.643][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.647][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.650][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-24 12:43:33.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.653][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.657][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.660][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:33.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:33.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.663][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:33.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.678][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-24 12:43:33.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:33.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:33.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:33.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.701][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.712][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.721][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:33.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:33.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:33.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.744][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-06-24 12:43:33.745][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.748][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.752][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.755][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.758][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:33.759][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:33.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:33.776][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-06-24 12:43:33.777][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-06-24 12:43:33.778][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-06-24 12:43:33.780][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.781][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.782][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:33.783][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.784][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:33.785][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:33.786][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:33.787][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:33.788][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:33.789][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:33.790][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-24 12:43:33.791][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.795][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.801][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.805][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.816][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.821][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.824][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:33.825][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:33.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.842][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.846][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.856][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.860][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.863][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-06-24 12:43:33.864][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:33.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.875][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[2024-06-24 12:43:33.881][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-06-24 12:43:33.882][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-06-24 12:43:33.883][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-06-24 12:43:33.885][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.887][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.888][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-24 12:43:33.889][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-24 12:43:33.890][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-24 12:43:33.891][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-24 12:43:33.892][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-24 12:43:33.893][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-24 12:43:33.894][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-24 12:43:33.895][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-24 12:43:33.896][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-24 12:43:33.898][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.905][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.908][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.915][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.932][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-06-24 12:43:33.933][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2024-06-24 12:43:33.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:33.945][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.948][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.952][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.956][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.959][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:33.966][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-24 12:43:33.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-24 12:43:33.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:33.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:33.970][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-24 12:43:33.971][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-24 12:43:33.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:33.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:33.989][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:33.991][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-06-24 12:43:33.992][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-06-24 12:43:33.993][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:33.993][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:33.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:33.995][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:33.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:33.996][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:33.997][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
  8.425   0.524  20.388

Example timings