Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-04-22 13:15 -0400 (Tue, 22 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
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 207/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbHmdb 1.14.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: biodbHmdb |
Version: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2025-04-21 19:21:11 -0400 (Mon, 21 Apr 2025) |
EndedAt: 2025-04-21 19:22:20 -0400 (Mon, 21 Apr 2025) |
EllapsedTime: 69.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: biodbHmdb.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbHmdb/DESCRIPTION’ ... OK * this is package ‘biodbHmdb’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbHmdb’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘zip’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck/00check.log’ for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘biodbHmdb’ ... ** this is package ‘biodbHmdb’ version ‘1.14.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EntryMaker.cpp -o EntryMaker.o EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor] accession_tag("<accession>", "</accession>"), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ closed(true) 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileEntryMaker.cpp -o FileEntryMaker.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TagDetector.cpp -o TagDetector.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XmlSplitter.cpp -o XmlSplitter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractXmlEntries.cpp -o extractXmlEntries.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-100-TagDetector.cpp -o test-100-TagDetector.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help No man pages found in package ‘biodbHmdb’ *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbHmdb) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbHmdb") biodb.INFO [2025-04-21 19:21:54.996][biodb::testContext] biodb.INFO [2025-04-21 19:21:55.001][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:21:55.003][biodb::testContext] Test context - Tests of independent functions biodb.INFO [2025-04-21 19:21:55.004][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:21:55.006][biodb::testContext] biodb.INFO [2025-04-21 19:21:55.008][biodb::testThat] biodb.INFO [2025-04-21 19:21:55.009][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. "). biodb.INFO [2025-04-21 19:21:55.011][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:55.012][biodb::testThat] biodb.INFO [2025-04-21 19:21:55.157][biodb::testContext] biodb.INFO [2025-04-21 19:21:55.158][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:21:55.160][biodb::testContext] Test context - Generic tests biodb.INFO [2025-04-21 19:21:55.161][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:21:55.162][biodb::testContext] biodb.INFO [2025-04-21 19:21:55.172][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0. biodb.DEBUG[2025-04-21 19:21:55.174][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-04-21 19:21:55.182][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:21:55.184][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-04-21 19:21:55.185][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-04-21 19:21:55.186][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.189][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-04-21 19:21:55.217][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-04-21 19:21:55.218][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.221][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-04-21 19:21:55.223][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-04-21 19:21:55.224][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.227][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-04-21 19:21:55.228][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-04-21 19:21:55.229][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-04-21 19:21:55.230][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.233][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-04-21 19:21:55.234][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-04-21 19:21:55.235][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-04-21 19:21:55.236][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.239][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-04-21 19:21:55.240][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-04-21 19:21:55.241][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.244][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-04-21 19:21:55.245][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-04-21 19:21:55.247][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-04-21 19:21:55.248][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.251][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-04-21 19:21:55.252][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-04-21 19:21:55.253][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.256][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-04-21 19:21:55.257][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-04-21 19:21:55.258][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-04-21 19:21:55.259][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.262][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-04-21 19:21:55.263][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-04-21 19:21:55.265][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-04-21 19:21:55.266][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-04-21 19:21:55.266][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-04-21 19:21:55.268][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-04-21 19:21:55.269][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.271][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[2025-04-21 19:21:55.272][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-04-21 19:21:55.273][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-04-21 19:21:55.274][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.278][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-04-21 19:21:55.279][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-04-21 19:21:55.280][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.283][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-04-21 19:21:55.284][self$set] Set key offline to FALSE. biodb.DEBUG[2025-04-21 19:21:55.286][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.289][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-04-21 19:21:55.290][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-04-21 19:21:55.291][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.293][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[2025-04-21 19:21:55.294][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-04-21 19:21:55.296][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-04-21 19:21:55.297][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.300][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-04-21 19:21:55.301][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-04-21 19:21:55.328][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-04-21 19:21:55.330][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.334][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-04-21 19:21:55.335][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-04-21 19:21:55.336][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-04-21 19:21:55.337][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.343][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-04-21 19:21:55.381][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.401][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-04-21 19:21:55.402][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.404][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:21:55.405][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:21:55.407][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:21:55.410][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-04-21 19:21:55.411][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:21:55.412][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.414][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-04-21 19:21:55.415][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:21:55.416][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.417][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.418][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:21:55.418][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-04-21 19:21:55.418][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-04-21 19:21:55.418][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-04-21 19:21:55.418][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-04-21 19:21:55.420][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:21:55.421][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.424][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:21:55.425][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.427][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:21:55.428][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.429][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:21:55.430][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:21:55.438][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.440][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.441][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-04-21 19:21:55.443][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.444][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-04-21 19:21:55.445][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.447][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:21:55.447][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:21:55.449][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:21:55.452][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-04-21 19:21:55.453][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:21:55.454][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.456][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-04-21 19:21:55.457][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:21:55.458][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.459][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.461][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:21:55.461][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-04-21 19:21:55.461][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-04-21 19:21:55.461][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-04-21 19:21:55.461][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-04-21 19:21:55.462][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:21:55.463][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.465][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:21:55.466][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.468][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:21:55.469][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.470][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:21:55.471][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:21:55.472][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.473][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.474][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-04-21 19:21:55.476][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.477][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-04-21 19:21:55.478][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.480][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:21:55.481][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.482][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:21:55.483][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.484][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:21:55.485][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-04-21 19:21:55.486][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:21:55.487][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.489][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-04-21 19:21:55.490][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:21:55.491][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.493][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.494][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.495][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:21:55.496][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.499][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:21:55.500][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.503][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:21:55.504][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.505][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:21:55.506][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:21:55.507][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.508][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.509][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-04-21 19:21:55.511][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.512][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-04-21 19:21:55.513][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.515][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:21:55.516][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:21:55.518][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:21:55.520][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-04-21 19:21:55.521][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:21:55.523][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.524][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-04-21 19:21:55.526][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:21:55.527][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.528][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:21:55.529][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.531][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:21:55.532][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.535][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:21:55.536][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:55.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:55.538][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:21:55.539][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.541][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:21:55.542][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:21:55.543][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:55.544][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:55.549][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:21:55.551][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.552][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[2025-04-21 19:21:55.553][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.559][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.564][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.569][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.574][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.577][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[2025-04-21 19:21:55.579][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.584][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.589][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.595][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.600][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.606][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.611][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.616][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.626][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.629][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[2025-04-21 19:21:55.630][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.635][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.639][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-04-21 19:21:55.650][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-04-21 19:21:55.652][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-04-21 19:21:55.653][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-04-21 19:21:55.655][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-04-21 19:21:55.656][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-04-21 19:21:55.657][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-04-21 19:21:55.659][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-04-21 19:21:55.660][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-04-21 19:21:55.662][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-04-21 19:21:55.713][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-04-21 19:21:55.716][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-04-21 19:21:55.718][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-04-21 19:21:55.720][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-04-21 19:21:55.722][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-04-21 19:21:55.723][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-04-21 19:21:55.725][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-04-21 19:21:55.727][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-04-21 19:21:55.729][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-04-21 19:21:55.731][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-04-21 19:21:55.733][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-04-21 19:21:55.735][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-04-21 19:21:55.737][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-04-21 19:21:55.738][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-04-21 19:21:55.740][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-04-21 19:21:55.742][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-04-21 19:21:55.744][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-04-21 19:21:55.745][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-04-21 19:21:55.748][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-04-21 19:21:55.750][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-04-21 19:21:55.752][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-04-21 19:21:55.754][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-04-21 19:21:55.755][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-04-21 19:21:55.757][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-04-21 19:21:55.759][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-04-21 19:21:55.761][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-04-21 19:21:55.763][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-04-21 19:21:55.764][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-04-21 19:21:55.766][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-04-21 19:21:55.768][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-04-21 19:21:55.769][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-04-21 19:21:55.771][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-04-21 19:21:55.774][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-04-21 19:21:55.776][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-04-21 19:21:55.777][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-04-21 19:21:55.779][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-04-21 19:21:55.781][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-04-21 19:21:55.782][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-04-21 19:21:55.784][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-04-21 19:21:55.786][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-04-21 19:21:55.787][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-04-21 19:21:55.789][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-04-21 19:21:55.790][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-04-21 19:21:55.792][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-04-21 19:21:55.793][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-04-21 19:21:55.795][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-04-21 19:21:55.797][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-04-21 19:21:55.799][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-04-21 19:21:55.801][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-04-21 19:21:55.802][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-04-21 19:21:55.804][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-04-21 19:21:55.806][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-04-21 19:21:55.808][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-04-21 19:21:55.810][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-04-21 19:21:55.811][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-04-21 19:21:55.813][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-04-21 19:21:55.814][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-04-21 19:21:55.816][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-04-21 19:21:55.817][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-04-21 19:21:55.819][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-04-21 19:21:55.821][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-04-21 19:21:55.822][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-04-21 19:21:55.824][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-04-21 19:21:55.825][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-04-21 19:21:55.827][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-04-21 19:21:55.829][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-04-21 19:21:55.831][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-04-21 19:21:55.832][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-04-21 19:21:55.834][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-04-21 19:21:55.847][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-04-21 19:21:55.849][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-04-21 19:21:55.851][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-04-21 19:21:55.853][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-04-21 19:21:55.861][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-04-21 19:21:55.864][initialize] This is biodb version 1.16.0. biodb.DEBUG[2025-04-21 19:21:55.868][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:21:55.869][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.875][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[2025-04-21 19:21:55.882][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.898][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.905][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.911][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[2025-04-21 19:21:55.912][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.919][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.927][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.969][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.976][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.984][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:55.992][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:55.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:55.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:55.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:55.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:55.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:55.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.000][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.008][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.016][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.023][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.029][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.036][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.044][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:21:56.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:21:56.052][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/definitions.yml". biodb.DEBUG[2025-04-21 19:21:56.067][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:21:56.070][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:21:56.071][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-04-21 19:21:56.073][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:21:56.074][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:21:56.075][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-04-21 19:21:56.076][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2025-04-21 19:21:56.077][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-04-21 19:21:56.078][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:21:56.079][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-04-21 19:21:56.081][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:21:56.082][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:21:56.083][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2025-04-21 19:21:56.084][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2025-04-21 19:21:56.085][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2025-04-21 19:21:56.087][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-04-21 19:21:56.088][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:21:56.088][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2025-04-21 19:21:56.088][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2025-04-21 19:21:56.089][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-04-21 19:21:56.090][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:56.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:56.092][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:21:56.093][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:21:56.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:21:56.095][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:21:56.097][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2025-04-21 19:21:56.097][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2025-04-21 19:21:56.098][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:21:56.099][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:21:56.101][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-04-21 19:21:56.102][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:21:56.110][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2025-04-21 19:21:56.112][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-04-21 19:21:56.114][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-04-21 19:21:56.117][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-04-21 19:21:56.119][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-04-21 19:21:56.149][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:21:56.150][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2025-04-21 19:21:56.155][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:21:56.161][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:21:56.166][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:21:56.168][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:21:56.170][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2025-04-21 19:21:56.171][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.DEBUG[2025-04-21 19:21:56.173][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2025-04-21 19:21:56.173][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip". biodb.DEBUG[2025-04-21 19:21:56.175][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:21:56.176][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:21:56.176][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler. biodb.DEBUG[2025-04-21 19:21:56.177][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize". biodb.DEBUG[2025-04-21 19:21:56.178][self$registerConnector] Register connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:21:56.210][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:21:56.212][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:21:56.213][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:21:56.215][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:21:56.217][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:21:56.219][self$setFrequency] t=1.000000, n=3.000000 biodb.INFO [2025-04-21 19:21:56.229][biodb::testThat] biodb.INFO [2025-04-21 19:21:56.231][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-04-21 19:21:56.233][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:56.234][biodb::testThat] biodb.TRACE[2025-04-21 19:21:56.240][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml". biodb.DEBUG[2025-04-21 19:21:56.242][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:21:56.245][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:21:56.256][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:21:56.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:56.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:56.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:56.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:56.271][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:56.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:21:56.288][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.289][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.291][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.292][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.318][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.319][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.320][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.321][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.355][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.362][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:56.364][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:56.365][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.366][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.368][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:56.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:56.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.373][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:56.374][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:56.375][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.376][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:56.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.383][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.385][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.386][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.387][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.395][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.396][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.398][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.399][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.406][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.407][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.408][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.410][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.412][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.424][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.426][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.427][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.428][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.429][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.435][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.436][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.437][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.438][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.439][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.443][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.444][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.445][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.447][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.453][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:56.454][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:56.455][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.456][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:56.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:56.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.462][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:56.463][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:56.464][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.465][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:56.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:56.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.471][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.473][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.474][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.475][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.481][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.482][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.483][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.484][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.491][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.493][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.494][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.495][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.502][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:56.503][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:56.504][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.506][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.507][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:56.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:56.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.512][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:56.514][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:56.515][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.516][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:56.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:56.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.523][ef$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:21:56.524][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.526][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.527][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.529][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:21:56.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.595][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:56.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:56.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.599][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:56.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:56.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.604][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:56.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:56.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.609][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:56.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:56.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.613][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:56.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:56.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.618][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:56.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:56.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:56.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.658][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:56.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.678][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:56.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:56.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.697][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:56.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:56.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.701][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:56.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:56.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.705][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:56.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:56.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:56.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:56.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:56.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:56.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:56.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:56.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:56.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:56.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:56.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:56.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:56.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:56.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.757][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:56.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:56.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.808][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.813][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:56.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.823][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.828][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.833][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:56.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.838][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:56.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:56.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.843][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:56.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:56.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.848][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:56.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:56.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.853][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:21:56.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:56.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.873][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:21:56.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:56.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:56.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:56.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.920][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:56.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:56.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.924][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:56.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:56.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.932][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:56.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:56.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:56.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:56.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:56.971][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001. biodb.TRACE[2025-04-21 19:21:56.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-04-21 19:21:56.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-04-21 19:21:56.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.977][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-04-21 19:21:56.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-04-21 19:21:56.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.981][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-04-21 19:21:56.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-04-21 19:21:56.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:56.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-04-21 19:21:56.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-04-21 19:21:56.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:56.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.078][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.083][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.088][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:57.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.113][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.114][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.115][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.117][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.141][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.154][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.159][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.160][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.162][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.163][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.164][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.195][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.196][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.197][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.198][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.215][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.221][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.224][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.229][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.230][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.231][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.231][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.265][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.266][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.267][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.269][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.292][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.297][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.302][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.304][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.305][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.306][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.307][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:57.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:57.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:57.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:57.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:57.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:57.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.345][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:57.347][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:57.348][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.350][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:57.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:57.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.365][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:57.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.370][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:57.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:57.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.375][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:57.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:57.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.380][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:57.382][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:57.383][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.385][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:57.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:57.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:57.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:57.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:57.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:57.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:57.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:57.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.416][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:57.417][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:57.418][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.419][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:57.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:57.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.436][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:57.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:57.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.441][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:57.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:57.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:57.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:57.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.451][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:57.452][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:57.453][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.454][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.455][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:57.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:57.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.487][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.489][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.490][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.491][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.524][ef$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.532][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.533][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.534][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.566][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.568][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.569][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.570][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.587][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.604][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.605][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.606][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.607][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:57.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:57.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.630][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:57.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:57.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.641][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:57.642][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:57.643][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.644][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.645][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:57.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:57.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:57.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:57.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:57.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:57.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:57.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:57.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.677][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:57.678][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:57.680][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.681][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:57.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:57.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:57.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:57.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:57.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:57.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:57.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:57.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.714][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:57.715][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:57.717][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.718][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:57.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:57.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.744][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:57.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:57.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.750][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:57.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:57.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.755][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:57.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:57.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.760][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:57.761][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:57.762][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.764][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.765][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:57.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:57.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.782][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:57.784][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:57.785][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.786][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.794][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:57.795][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:57.797][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.798][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.805][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:57.807][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:57.809][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.810][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.817][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.818][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:57.819][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.820][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.827][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.829][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:57.830][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.831][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.839][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.841][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:57.842][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.844][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.851][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.853][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:57.854][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.855][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.863][ef$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.864][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:57.866][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.867][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.875][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:57.876][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:57.878][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.879][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.887][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:57.888][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:57.890][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.891][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.899][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:57.900][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:57.902][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.903][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.911][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:57.912][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:57.914][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.915][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.923][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.925][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:57.926][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.928][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.935][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.937][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:57.938][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.940][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.953][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:57.954][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:57.956][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.958][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.964][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.965][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:57.966][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.967][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.973][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.975][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:57.976][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.976][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:57.987][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:57.988][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:57.989][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:57.990][ef$get] fields variable is a list. biodb.INFO [2025-04-21 19:21:58.002][biodb::testThat] biodb.INFO [2025-04-21 19:21:58.004][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-04-21 19:21:58.005][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:58.006][biodb::testThat] biodb.DEBUG[2025-04-21 19:21:58.021][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2025-04-21 19:21:58.028][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2025-04-21 19:21:58.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:58.073][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2025-04-21 19:21:58.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001". biodb.TRACE[2025-04-21 19:21:58.077][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-04-21 19:21:58.102][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml". biodb.DEBUG[2025-04-21 19:21:58.104][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2025-04-21 19:21:58.136][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:21:58.138][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:21:58.139][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:21:58.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:21:58.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:21:58.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:21:58.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:21:58.154][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:21:58.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:21:58.161][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.163][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.164][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.165][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.170][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.172][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.173][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.174][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.175][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.180][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:58.181][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:58.182][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.183][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.185][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:58.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:58.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.191][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:58.192][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:58.193][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.202][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.204][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:58.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:58.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.209][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.210][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.212][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.212][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.219][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.220][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.222][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.227][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.235][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.237][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.238][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.239][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.243][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.249][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.251][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.252][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.253][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.260][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.262][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.263][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.264][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.271][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.272][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.274][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.275][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.277][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.281][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:58.282][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:58.284][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.285][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:58.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.291][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:58.292][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:58.293][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.294][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:58.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.300][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.301][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.302][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.303][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.311][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.312][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.313][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.315][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.322][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.323][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.324][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.326][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.333][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:58.337][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:58.338][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.339][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:58.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:58.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.346][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:58.347][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:58.348][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.349][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:58.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.360][ef$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:21:58.363][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.364][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.366][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.368][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:21:58.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.388][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:58.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:58.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.399][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:58.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:58.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.405][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:21:58.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:21:58.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.410][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:58.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:58.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.416][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:58.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:58.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.421][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:21:58.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:21:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:21:58.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:21:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.477][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:21:58.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.493][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:21:58.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:21:58.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:58.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.519][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:58.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:58.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:58.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:58.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:58.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:58.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:58.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:21:58.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:21:58.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:58.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:58.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:58.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:21:58.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:21:58.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.588][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:21:58.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:21:58.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.648][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:21:58.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.653][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.659][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.664][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:58.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:58.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:58.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.679][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:58.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.684][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:21:58.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:21:58.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.689][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:21:58.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:21:58.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.712][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:21:58.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:21:58.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:58.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:58.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.748][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.758][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:58.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:21:58.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:21:58.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:21:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:58.803][self$createEntryFromContent] Accession numbers: HMDB0000001. biodb.TRACE[2025-04-21 19:21:58.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2025-04-21 19:21:58.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2025-04-21 19:21:58.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2025-04-21 19:21:58.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2025-04-21 19:21:58.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2025-04-21 19:21:58.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2025-04-21 19:21:58.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-04-21 19:21:58.830][biodb::testThat] biodb.INFO [2025-04-21 19:21:58.832][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-04-21 19:21:58.833][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:58.834][biodb::testThat] biodb.TRACE[2025-04-21 19:21:58.839][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.840][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.841][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.843][ef$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:58.844][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name". biodb.TRACE[2025-04-21 19:21:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:58.921][function(conn, opt)] With value "1-Methylhistidine". biodb.DEBUG[2025-04-21 19:21:58.923][private$doSearchForEntries] fields NAMES = name biodb.DEBUG[2025-04-21 19:21:58.924][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2025-04-21 19:21:58.926][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2025-04-21 19:21:58.928][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:58.931][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:58.933][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:21:58.935][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:58.936][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:21:58.938][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:21:58.940][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:21:58.941][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:21:58.943][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:21:58.944][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:21:58.945][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2025-04-21 19:21:58.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:58.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:58.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:58.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:58.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:58.965][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:21:58.966][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:21:58.968][function(conn, opt)] With found IDs [1]: "HMDB0000001". biodb.TRACE[2025-04-21 19:21:58.998][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.000][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.001][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.003][ef$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.005][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description". biodb.TRACE[2025-04-21 19:21:59.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.044][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.049][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.058][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.". biodb.DEBUG[2025-04-21 19:21:59.124][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2025-04-21 19:21:59.126][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat. biodb.DEBUG[2025-04-21 19:21:59.127][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat. biodb.DEBUG[2025-04-21 19:21:59.147][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.149][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.154][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:21:59.156][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.157][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:21:59.187][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:21:59.189][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:21:59.190][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:21:59.191][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:21:59.193][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:21:59.194][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2025-04-21 19:21:59.196][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.201][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.207][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.213][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:21:59.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:21:59.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.218][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:21:59.219][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:21:59.220][function(conn, opt)] With found IDs [1]: "HMDB0000001". biodb.TRACE[2025-04-21 19:21:59.246][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.247][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.249][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.252][ef$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.255][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions". biodb.TRACE[2025-04-21 19:21:59.274][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.281][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.287][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.295][function(conn, opt)] With value "HMDB00001". biodb.DEBUG[2025-04-21 19:21:59.297][private$doSearchForEntries] fields NAMES = secondary.accessions biodb.DEBUG[2025-04-21 19:21:59.298][private$doSearchForEntries] fields VALUES = HMDB00001 biodb.DEBUG[2025-04-21 19:21:59.299][private$doSearchForEntries] fields VALUES = HMDB00001 biodb.DEBUG[2025-04-21 19:21:59.301][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.303][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.304][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:21:59.306][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.311][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:21:59.314][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:21:59.316][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:21:59.317][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:21:59.318][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:21:59.320][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:21:59.321][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2025-04-21 19:21:59.323][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.338][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.344][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:21:59.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.349][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:21:59.350][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:21:59.351][function(conn, opt)] With found IDs [1]: "HMDB0000001". biodb.INFO [2025-04-21 19:21:59.375][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.376][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-04-21 19:21:59.378][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:59.379][biodb::testThat] biodb.TRACE[2025-04-21 19:21:59.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.442][private$doSearchForEntries] fields NAMES = name biodb.DEBUG[2025-04-21 19:21:59.443][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2025-04-21 19:21:59.445][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2025-04-21 19:21:59.447][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.449][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.451][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:21:59.453][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:21:59.454][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:21:59.456][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:21:59.457][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:21:59.459][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:21:59.460][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:21:59.461][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:21:59.463][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2025-04-21 19:21:59.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:21:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:21:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:21:59.497][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:21:59.500][private$doSearchForEntries] COUNT IDS = 1 biodb.INFO [2025-04-21 19:21:59.525][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.526][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-04-21 19:21:59.528][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:59.529][biodb::testThat] biodb.TRACE[2025-04-21 19:21:59.556][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-04-21 19:21:59.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-04-21 19:21:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-04-21 19:21:59.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-04-21 19:21:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.642][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-04-21 19:21:59.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.647][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-04-21 19:21:59.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-04-21 19:21:59.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:21:59.656][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-04-21 19:21:59.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-04-21 19:21:59.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:21:59.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-04-21 19:21:59.672][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.673][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-04-21 19:21:59.675][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:59.676][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.687][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.689][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-04-21 19:21:59.690][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:59.692][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.704][biodb::testThat] biodb.INFO [2025-04-21 19:21:59.705][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-04-21 19:21:59.713][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:21:59.714][biodb::testThat] biodb.DEBUG[2025-04-21 19:21:59.720][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001". biodb.DEBUG[2025-04-21 19:22:07.934][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001. biodb.INFO [2025-04-21 19:22:07.991][biodb::testThat] biodb.INFO [2025-04-21 19:22:07.992][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-04-21 19:22:07.994][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:07.995][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:08.179][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png. biodb.TRACE[2025-04-21 19:22:08.214][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:08.216][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:08.217][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.219][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.220][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:08.222][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:08.224][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.225][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.226][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:08.227][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:08.229][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.230][ef$get] fields variable is a list. biodb.INFO [2025-04-21 19:22:08.232][biodb::testThat] biodb.INFO [2025-04-21 19:22:08.233][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2025-04-21 19:22:08.234][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:08.235][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:08.237][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2025-04-21 19:22:08.305][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2025-04-21 19:22:08.308][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.310][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2025-04-21 19:22:08.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA". biodb.TRACE[2025-04-21 19:22:08.333][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-04-21 19:22:08.334][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-04-21 19:22:08.336][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2025-04-21 19:22:08.338][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.339][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:22:08.341][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:22:08.343][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:08.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:08.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:08.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:08.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:08.355][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:22:08.359][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:08.440][self$createEntryFromContent] Accession numbers: NA. biodb.DEBUG[2025-04-21 19:22:08.441][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2025-04-21 19:22:08.463][biodb::testThat] biodb.INFO [2025-04-21 19:22:08.465][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2025-04-21 19:22:08.467][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:08.468][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:08.479][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001" biodb.DEBUG[2025-04-21 19:22:08.481][private$loadEntries] Creating entries from ids [1]: "WRONGB". biodb.DEBUG[2025-04-21 19:22:08.482][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2025-04-21 19:22:08.484][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.486][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2025-04-21 19:22:08.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB". biodb.TRACE[2025-04-21 19:22:08.490][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-04-21 19:22:08.492][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-04-21 19:22:08.494][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2025-04-21 19:22:08.496][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.498][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:22:08.499][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:22:08.501][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:08.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:08.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:08.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:08.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:08.511][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:22:08.513][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.518][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:08.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:08.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:08.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:08.551][self$createEntryFromContent] Accession numbers: NA. biodb.DEBUG[2025-04-21 19:22:08.552][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2025-04-21 19:22:08.553][function(conn, opt)] Entries: [2]: "NULL, <environment>" biodb.INFO [2025-04-21 19:22:08.579][biodb::testThat] biodb.INFO [2025-04-21 19:22:08.581][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2025-04-21 19:22:08.582][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:08.583][biodb::testThat] biodb.INFO [2025-04-21 19:22:08.611][biodb::testThat] biodb.INFO [2025-04-21 19:22:08.613][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2025-04-21 19:22:08.615][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:08.616][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:08.619][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.620][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.622][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:22:08.624][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.625][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:22:08.627][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:22:08.628][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:22:08.629][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:22:08.630][private$doGetEntryIds] COUNT IDS = 2 biodb.INFO [2025-04-21 19:22:08.642][biodb::testThat] biodb.INFO [2025-04-21 19:22:08.643][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2025-04-21 19:22:08.645][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:08.646][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:08.649][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.651][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.653][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:22:08.655][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:08.656][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:22:08.657][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:22:08.659][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:22:08.660][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:22:08.661][private$doGetEntryIds] COUNT IDS = 2 biodb.TRACE[2025-04-21 19:22:08.674][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:08.675][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:08.677][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.678][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.679][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:08.680][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:08.682][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.683][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:08.684][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:08.685][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:08.686][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:08.688][ef$get] fields variable is a list. biodb.INFO [2025-04-21 19:22:08.689][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-04-21 19:22:08.691][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2025-04-21 19:22:08.703][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2025-04-21 19:22:08.704][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-04-21 19:22:08.705][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:08.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:08.707][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:08.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:08.710][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-04-21 19:22:08.715][biodb::testContext] biodb.INFO [2025-04-21 19:22:08.717][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:22:08.718][biodb::testContext] Test context - Test retrieval of entries biodb.INFO [2025-04-21 19:22:08.724][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:22:08.725][biodb::testContext] biodb.INFO [2025-04-21 19:22:08.732][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0. biodb.DEBUG[2025-04-21 19:22:08.734][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-04-21 19:22:08.739][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:22:08.740][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-04-21 19:22:08.741][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-04-21 19:22:08.743][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.746][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-04-21 19:22:08.747][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-04-21 19:22:08.748][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.751][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-04-21 19:22:08.752][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-04-21 19:22:08.753][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.757][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-04-21 19:22:08.757][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-04-21 19:22:08.759][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-04-21 19:22:08.760][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.764][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-04-21 19:22:08.765][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-04-21 19:22:08.766][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-04-21 19:22:08.767][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.771][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-04-21 19:22:08.773][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-04-21 19:22:08.774][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.777][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-04-21 19:22:08.779][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-04-21 19:22:08.780][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-04-21 19:22:08.781][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.785][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-04-21 19:22:08.786][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-04-21 19:22:08.787][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.789][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-04-21 19:22:08.790][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-04-21 19:22:08.792][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-04-21 19:22:08.793][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.797][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-04-21 19:22:08.798][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-04-21 19:22:08.799][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-04-21 19:22:08.800][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-04-21 19:22:08.802][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-04-21 19:22:08.803][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-04-21 19:22:08.805][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.807][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[2025-04-21 19:22:08.808][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-04-21 19:22:08.809][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-04-21 19:22:08.810][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.814][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-04-21 19:22:08.815][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-04-21 19:22:08.816][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.820][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-04-21 19:22:08.822][self$set] Set key offline to FALSE. biodb.DEBUG[2025-04-21 19:22:08.823][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.826][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-04-21 19:22:08.827][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-04-21 19:22:08.828][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.832][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-04-21 19:22:08.833][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-04-21 19:22:08.834][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.837][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-04-21 19:22:08.838][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-04-21 19:22:08.862][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-04-21 19:22:08.864][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.867][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[2025-04-21 19:22:08.868][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-04-21 19:22:08.869][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-04-21 19:22:08.871][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-04-21 19:22:08.872][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:08.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:08.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:08.876][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-04-21 19:22:08.879][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.880][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-04-21 19:22:08.882][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.883][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:08.884][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.893][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:08.895][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:08.899][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-04-21 19:22:08.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:08.903][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.904][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-04-21 19:22:08.905][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:08.907][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.908][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.910][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:22:08.910][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-04-21 19:22:08.910][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-04-21 19:22:08.910][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-04-21 19:22:08.910][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-04-21 19:22:08.911][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:08.912][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:08.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:08.915][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:08.916][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:08.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:08.918][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:08.920][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.920][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:08.921][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:08.922][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.923][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.925][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-04-21 19:22:08.927][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.928][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-04-21 19:22:08.929][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.931][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:08.932][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:08.934][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.936][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:08.937][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-04-21 19:22:08.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:08.939][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.941][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-04-21 19:22:08.942][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:08.943][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.944][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.945][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:22:08.945][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-04-21 19:22:08.945][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-04-21 19:22:08.945][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-04-21 19:22:08.945][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-04-21 19:22:08.947][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:08.948][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:08.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:08.950][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:08.951][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:08.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:08.954][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:08.955][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.956][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:08.958][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:08.959][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.960][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.962][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-04-21 19:22:08.964][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.966][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-04-21 19:22:08.967][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.968][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:08.970][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.971][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:08.973][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.974][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:08.975][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-04-21 19:22:08.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:08.977][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.979][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-04-21 19:22:08.980][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:08.981][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.982][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:08.983][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.984][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:08.986][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:08.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:08.988][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:08.990][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:08.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:08.992][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:08.993][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:08.995][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:08.996][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:08.997][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:08.998][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:09.000][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-04-21 19:22:09.002][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.003][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-04-21 19:22:09.004][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.006][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:09.007][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:09.010][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:09.012][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:09.013][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-04-21 19:22:09.015][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:09.016][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:09.017][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-04-21 19:22:09.019][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:09.020][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:09.022][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.023][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:09.024][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:09.025][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:09.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:09.028][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:09.029][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:09.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:09.038][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:09.039][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:09.041][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:09.042][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:09.044][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:09.045][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:09.047][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:22:09.048][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.051][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.057][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.061][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.DEBUG[2025-04-21 19:22:09.063][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.068][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.074][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.080][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.086][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.092][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.097][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.102][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.107][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.113][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.118][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.124][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.130][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.136][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.141][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.147][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-04-21 19:22:09.149][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-04-21 19:22:09.150][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-04-21 19:22:09.152][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-04-21 19:22:09.154][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-04-21 19:22:09.156][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-04-21 19:22:09.157][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-04-21 19:22:09.159][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-04-21 19:22:09.161][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-04-21 19:22:09.163][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-04-21 19:22:09.164][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-04-21 19:22:09.166][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-04-21 19:22:09.168][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-04-21 19:22:09.176][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-04-21 19:22:09.180][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-04-21 19:22:09.182][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-04-21 19:22:09.185][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-04-21 19:22:09.188][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-04-21 19:22:09.191][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-04-21 19:22:09.192][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-04-21 19:22:09.194][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-04-21 19:22:09.196][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-04-21 19:22:09.197][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-04-21 19:22:09.199][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-04-21 19:22:09.201][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-04-21 19:22:09.203][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-04-21 19:22:09.204][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-04-21 19:22:09.206][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-04-21 19:22:09.208][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-04-21 19:22:09.210][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-04-21 19:22:09.212][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-04-21 19:22:09.214][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-04-21 19:22:09.215][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-04-21 19:22:09.217][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-04-21 19:22:09.219][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-04-21 19:22:09.221][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-04-21 19:22:09.222][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-04-21 19:22:09.224][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-04-21 19:22:09.226][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-04-21 19:22:09.228][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-04-21 19:22:09.230][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-04-21 19:22:09.232][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-04-21 19:22:09.234][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-04-21 19:22:09.235][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-04-21 19:22:09.237][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-04-21 19:22:09.239][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-04-21 19:22:09.241][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-04-21 19:22:09.242][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-04-21 19:22:09.244][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-04-21 19:22:09.246][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-04-21 19:22:09.248][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-04-21 19:22:09.249][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-04-21 19:22:09.251][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-04-21 19:22:09.253][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-04-21 19:22:09.255][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-04-21 19:22:09.257][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-04-21 19:22:09.259][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-04-21 19:22:09.260][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-04-21 19:22:09.262][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-04-21 19:22:09.263][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-04-21 19:22:09.265][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-04-21 19:22:09.267][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-04-21 19:22:09.269][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-04-21 19:22:09.271][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-04-21 19:22:09.273][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-04-21 19:22:09.275][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-04-21 19:22:09.276][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-04-21 19:22:09.278][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-04-21 19:22:09.279][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-04-21 19:22:09.281][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-04-21 19:22:09.283][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-04-21 19:22:09.285][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-04-21 19:22:09.286][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-04-21 19:22:09.288][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-04-21 19:22:09.289][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-04-21 19:22:09.291][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-04-21 19:22:09.292][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-04-21 19:22:09.294][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-04-21 19:22:09.296][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-04-21 19:22:09.298][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-04-21 19:22:09.300][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-04-21 19:22:09.302][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-04-21 19:22:09.304][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-04-21 19:22:09.306][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-04-21 19:22:09.308][initialize] This is biodb version 1.16.0. biodb.DEBUG[2025-04-21 19:22:09.309][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:22:09.310][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.321][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.324][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.331][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.338][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.345][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.353][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.361][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.368][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.376][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.383][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.392][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.399][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.407][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.414][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[2025-04-21 19:22:09.415][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.424][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.431][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.438][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[2025-04-21 19:22:09.439][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.454][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:09.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:09.464][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/definitions.yml". biodb.DEBUG[2025-04-21 19:22:09.466][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:09.468][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:09.469][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-04-21 19:22:09.470][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.472][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:09.473][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:09.474][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2025-04-21 19:22:09.475][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:09.478][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-04-21 19:22:09.479][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:09.480][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.481][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2025-04-21 19:22:09.482][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2025-04-21 19:22:09.484][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2025-04-21 19:22:09.485][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-04-21 19:22:09.486][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:22:09.486][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2025-04-21 19:22:09.486][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2025-04-21 19:22:09.488][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-04-21 19:22:09.489][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:09.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:09.492][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:09.493][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:09.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:09.495][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:09.496][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2025-04-21 19:22:09.496][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2025-04-21 19:22:09.497][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:09.498][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:09.500][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:09.501][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:09.503][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2025-04-21 19:22:09.505][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-04-21 19:22:09.507][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-04-21 19:22:09.509][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-04-21 19:22:09.511][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-04-21 19:22:09.516][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:09.517][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2025-04-21 19:22:09.518][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:09.520][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:22:09.522][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:09.523][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:09.524][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2025-04-21 19:22:09.526][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.DEBUG[2025-04-21 19:22:09.527][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2025-04-21 19:22:09.527][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip". biodb.DEBUG[2025-04-21 19:22:09.528][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:09.529][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:09.530][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler. biodb.DEBUG[2025-04-21 19:22:09.531][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize". biodb.DEBUG[2025-04-21 19:22:09.532][self$registerConnector] Register connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:09.534][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:22:09.536][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:09.537][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:09.539][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:22:09.540][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:09.542][self$setFrequency] t=1.000000, n=3.000000 biodb.INFO [2025-04-21 19:22:09.546][biodb::testThat] biodb.INFO [2025-04-21 19:22:09.547][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. "). biodb.INFO [2025-04-21 19:22:09.550][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:09.551][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:09.555][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:09.556][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:09.558][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:22:09.560][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:09.561][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:22:09.563][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:22:09.564][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:22:09.565][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:22:09.566][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:22:09.570][conn$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.INFO [2025-04-21 19:22:09.577][biodb::testThat] biodb.INFO [2025-04-21 19:22:09.579][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. "). biodb.INFO [2025-04-21 19:22:09.580][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:09.582][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:09.584][private$loadEntries] Creating entries from ids [1]: "HMDB0000002". biodb.DEBUG[2025-04-21 19:22:09.586][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2025-04-21 19:22:09.588][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:09.589][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2025-04-21 19:22:09.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002". biodb.TRACE[2025-04-21 19:22:09.601][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-04-21 19:22:09.603][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml". biodb.DEBUG[2025-04-21 19:22:09.605][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2025-04-21 19:22:09.607][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:22:09.608][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:22:09.610][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:09.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:09.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:09.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:09.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:09.621][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:09.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:22:09.625][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:09.627][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:09.628][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.629][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:09.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:09.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.636][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:09.637][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:09.638][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.639][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.640][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:09.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:09.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.644][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:09.645][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:09.646][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.647][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.649][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:09.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:09.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.657][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:09.658][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:09.659][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.661][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.662][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:09.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:09.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.668][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.669][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.670][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.672][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.679][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.680][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.681][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.683][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.689][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:09.691][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:09.692][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.693][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.695][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:09.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:09.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.699][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:09.700][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:09.701][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.703][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:09.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:09.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.709][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.710][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.712][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.713][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.719][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.720][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.722][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.723][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.729][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:09.730][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:09.732][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.733][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:09.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:09.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.747][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:09.748][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:09.749][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.751][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:09.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:09.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.758][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:09.759][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:09.760][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.761][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:09.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:09.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.768][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:09.769][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:09.770][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.771][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:09.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:09.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.778][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:09.780][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:09.781][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.782][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:09.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:09.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.789][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:09.790][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:09.792][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.793][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.794][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.800][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:09.801][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:09.802][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.804][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.805][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:09.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:09.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.811][ef$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:22:09.812][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.814][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.815][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.816][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:22:09.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:09.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:09.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:09.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:09.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.838][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:09.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:09.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.844][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:09.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:09.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.849][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:09.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:09.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:09.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:09.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.857][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:09.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:09.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.862][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:09.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:09.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:09.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:09.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:09.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:09.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.938][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.950][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:09.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:09.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.960][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:09.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:09.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:09.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:09.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.976][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:09.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:09.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:09.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:09.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.987][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:09.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:09.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:09.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:09.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:09.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:09.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:09.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:10.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:10.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:10.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:10.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:10.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:10.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.022][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:10.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:10.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.033][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:10.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:10.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.039][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:10.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:10.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:10.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:10.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:10.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.075][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:10.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:10.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.082][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:10.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:10.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.088][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:10.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:10.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.093][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:10.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:10.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.099][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:10.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:10.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.105][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:10.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.110][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:10.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:10.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.115][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:10.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:10.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.120][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:10.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:10.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.125][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:22:10.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:10.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:10.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:10.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.147][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:22:10.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:10.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:10.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:10.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:10.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.195][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:10.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:10.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.206][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:10.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:10.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:10.243][self$createEntryFromContent] Accession numbers: HMDB0000002. biodb.TRACE[2025-04-21 19:22:10.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:10.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:10.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:10.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:10.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-04-21 19:22:10.271][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-04-21 19:22:10.273][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2025-04-21 19:22:10.275][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2025-04-21 19:22:10.276][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-04-21 19:22:10.277][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:10.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:10.279][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.282][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-04-21 19:22:10.288][biodb::testContext] biodb.INFO [2025-04-21 19:22:10.290][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:22:10.291][biodb::testContext] Test context - Test search of entries biodb.INFO [2025-04-21 19:22:10.292][biodb::testContext] ******************************************************************************** biodb.INFO [2025-04-21 19:22:10.293][biodb::testContext] biodb.INFO [2025-04-21 19:22:10.300][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0. biodb.DEBUG[2025-04-21 19:22:10.303][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-04-21 19:22:10.308][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:22:10.310][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-04-21 19:22:10.311][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-04-21 19:22:10.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.317][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-04-21 19:22:10.318][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-04-21 19:22:10.320][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.324][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-04-21 19:22:10.325][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-04-21 19:22:10.326][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.330][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-04-21 19:22:10.332][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-04-21 19:22:10.341][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-04-21 19:22:10.343][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.347][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-04-21 19:22:10.348][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-04-21 19:22:10.349][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-04-21 19:22:10.350][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.354][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-04-21 19:22:10.355][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-04-21 19:22:10.356][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.360][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-04-21 19:22:10.362][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-04-21 19:22:10.363][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-04-21 19:22:10.364][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.368][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-04-21 19:22:10.370][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-04-21 19:22:10.371][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.375][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-04-21 19:22:10.376][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-04-21 19:22:10.377][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-04-21 19:22:10.378][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.382][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-04-21 19:22:10.383][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-04-21 19:22:10.384][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-04-21 19:22:10.386][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-04-21 19:22:10.387][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-04-21 19:22:10.388][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-04-21 19:22:10.389][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.393][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-04-21 19:22:10.394][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-04-21 19:22:10.396][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.400][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-04-21 19:22:10.401][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-04-21 19:22:10.402][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.406][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-04-21 19:22:10.407][self$set] Set key offline to FALSE. biodb.DEBUG[2025-04-21 19:22:10.408][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.412][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-04-21 19:22:10.413][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-04-21 19:22:10.414][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.418][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-04-21 19:22:10.420][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-04-21 19:22:10.421][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.425][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-04-21 19:22:10.426][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-04-21 19:22:10.468][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-04-21 19:22:10.469][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.474][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-04-21 19:22:10.475][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-04-21 19:22:10.477][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-04-21 19:22:10.478][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.482][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-04-21 19:22:10.484][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.485][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-04-21 19:22:10.487][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.488][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:10.490][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:10.492][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.494][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:10.495][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-04-21 19:22:10.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:10.498][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.499][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-04-21 19:22:10.501][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:10.502][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.503][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.505][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:22:10.505][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-04-21 19:22:10.505][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-04-21 19:22:10.505][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-04-21 19:22:10.505][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-04-21 19:22:10.506][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:10.507][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.510][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:10.511][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.513][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:10.515][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.516][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:10.525][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:10.527][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.529][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.531][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-04-21 19:22:10.533][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.535][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-04-21 19:22:10.537][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.538][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:10.539][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:10.542][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.543][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:10.545][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-04-21 19:22:10.546][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:10.547][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.549][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-04-21 19:22:10.550][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:10.551][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.552][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.554][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:22:10.554][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-04-21 19:22:10.554][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-04-21 19:22:10.554][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-04-21 19:22:10.554][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-04-21 19:22:10.555][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:10.557][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.559][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:10.560][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.563][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:10.564][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.565][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:10.567][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:10.568][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.569][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.571][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-04-21 19:22:10.573][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.574][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-04-21 19:22:10.576][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.577][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:10.579][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:10.582][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:10.584][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-04-21 19:22:10.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:10.587][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.588][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-04-21 19:22:10.589][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:10.591][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.592][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.593][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.595][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:10.596][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.599][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:10.600][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.602][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:10.604][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.605][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:10.606][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:10.608][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.609][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.611][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-04-21 19:22:10.613][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.614][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-04-21 19:22:10.616][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.618][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:10.619][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.621][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-04-21 19:22:10.622][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.624][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:10.630][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-04-21 19:22:10.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:10.633][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.635][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-04-21 19:22:10.636][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:10.637][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.639][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-04-21 19:22:10.640][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.642][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-04-21 19:22:10.643][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.645][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:10.647][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:10.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:10.649][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:10.651][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.652][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:10.653][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:10.655][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:10.656][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:10.657][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:22:10.658][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.661][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.665][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[2025-04-21 19:22:10.666][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.681][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.688][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.696][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.702][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.709][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.715][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.722][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.728][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.734][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.740][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.746][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.752][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.758][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.764][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.770][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.776][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-04-21 19:22:10.778][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-04-21 19:22:10.780][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-04-21 19:22:10.782][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-04-21 19:22:10.784][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-04-21 19:22:10.785][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-04-21 19:22:10.787][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-04-21 19:22:10.789][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-04-21 19:22:10.791][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-04-21 19:22:10.793][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-04-21 19:22:10.795][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-04-21 19:22:10.797][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-04-21 19:22:10.799][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-04-21 19:22:10.801][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-04-21 19:22:10.802][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-04-21 19:22:10.804][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-04-21 19:22:10.806][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-04-21 19:22:10.808][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-04-21 19:22:10.810][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-04-21 19:22:10.811][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-04-21 19:22:10.813][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-04-21 19:22:10.815][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-04-21 19:22:10.825][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-04-21 19:22:10.828][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-04-21 19:22:10.830][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-04-21 19:22:10.832][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-04-21 19:22:10.834][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-04-21 19:22:10.836][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-04-21 19:22:10.838][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-04-21 19:22:10.840][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-04-21 19:22:10.842][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-04-21 19:22:10.844][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-04-21 19:22:10.846][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-04-21 19:22:10.848][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-04-21 19:22:10.850][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-04-21 19:22:10.852][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-04-21 19:22:10.854][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-04-21 19:22:10.856][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-04-21 19:22:10.858][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-04-21 19:22:10.860][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-04-21 19:22:10.862][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-04-21 19:22:10.864][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-04-21 19:22:10.866][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-04-21 19:22:10.868][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-04-21 19:22:10.870][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-04-21 19:22:10.872][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-04-21 19:22:10.874][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-04-21 19:22:10.876][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-04-21 19:22:10.878][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-04-21 19:22:10.879][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-04-21 19:22:10.881][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-04-21 19:22:10.883][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-04-21 19:22:10.885][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-04-21 19:22:10.887][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-04-21 19:22:10.889][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-04-21 19:22:10.892][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-04-21 19:22:10.894][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-04-21 19:22:10.895][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-04-21 19:22:10.897][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-04-21 19:22:10.899][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-04-21 19:22:10.901][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-04-21 19:22:10.903][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-04-21 19:22:10.905][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-04-21 19:22:10.906][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-04-21 19:22:10.908][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-04-21 19:22:10.910][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-04-21 19:22:10.912][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-04-21 19:22:10.914][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-04-21 19:22:10.916][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-04-21 19:22:10.918][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-04-21 19:22:10.919][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-04-21 19:22:10.921][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-04-21 19:22:10.922][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-04-21 19:22:10.924][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-04-21 19:22:10.926][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-04-21 19:22:10.927][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-04-21 19:22:10.929][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-04-21 19:22:10.931][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-04-21 19:22:10.933][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-04-21 19:22:10.935][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-04-21 19:22:10.937][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-04-21 19:22:10.939][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-04-21 19:22:10.941][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-04-21 19:22:10.943][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-04-21 19:22:10.945][initialize] This is biodb version 1.16.0. biodb.DEBUG[2025-04-21 19:22:10.946][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-04-21 19:22:10.947][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.949][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.951][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[2025-04-21 19:22:10.952][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:10.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:10.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.968][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:10.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:10.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.977][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:10.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:10.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.984][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:10.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:10.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:10.991][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:10.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:10.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:10.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:10.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:10.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:10.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.000][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.009][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.017][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.025][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.033][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.041][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.049][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.058][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.066][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.074][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.082][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.090][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-04-21 19:22:11.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.108][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/definitions.yml". biodb.DEBUG[2025-04-21 19:22:11.110][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:11.112][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-04-21 19:22:11.114][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-04-21 19:22:11.115][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-04-21 19:22:11.117][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-04-21 19:22:11.118][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-04-21 19:22:11.119][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2025-04-21 19:22:11.121][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:11.122][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-04-21 19:22:11.124][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-04-21 19:22:11.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-04-21 19:22:11.126][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-04-21 19:22:11.128][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2025-04-21 19:22:11.129][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2025-04-21 19:22:11.130][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2025-04-21 19:22:11.132][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-04-21 19:22:11.133][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-04-21 19:22:11.133][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2025-04-21 19:22:11.133][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2025-04-21 19:22:11.135][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-04-21 19:22:11.136][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:11.137][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:11.138][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-04-21 19:22:11.140][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-04-21 19:22:11.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-04-21 19:22:11.142][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-04-21 19:22:11.144][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2025-04-21 19:22:11.144][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2025-04-21 19:22:11.145][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:11.146][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:11.147][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-04-21 19:22:11.148][self$setPropertyValue] biodb.DEBUG[2025-04-21 19:22:11.150][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2025-04-21 19:22:11.152][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-04-21 19:22:11.154][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-04-21 19:22:11.156][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-04-21 19:22:11.158][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-04-21 19:22:11.162][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:11.163][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2025-04-21 19:22:11.165][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:11.167][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:22:11.169][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:11.170][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:11.172][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2025-04-21 19:22:11.173][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.DEBUG[2025-04-21 19:22:11.175][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2025-04-21 19:22:11.175][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip". biodb.DEBUG[2025-04-21 19:22:11.176][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-04-21 19:22:11.177][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-04-21 19:22:11.179][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler. biodb.DEBUG[2025-04-21 19:22:11.180][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize". biodb.DEBUG[2025-04-21 19:22:11.182][self$registerConnector] Register connector hmdb.metabolites. biodb.DEBUG[2025-04-21 19:22:11.184][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:22:11.185][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:11.186][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:11.188][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites". biodb.DEBUG[2025-04-21 19:22:11.190][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-04-21 19:22:11.191][self$setFrequency] t=1.000000, n=3.000000 biodb.INFO [2025-04-21 19:22:11.193][biodb::testThat] biodb.INFO [2025-04-21 19:22:11.194][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. "). biodb.INFO [2025-04-21 19:22:11.195][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-04-21 19:22:11.197][biodb::testThat] biodb.DEBUG[2025-04-21 19:22:11.199][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2025-04-21 19:22:11.201][private$doSearchForEntries] fields VALUES = and biodb.DEBUG[2025-04-21 19:22:11.202][private$doSearchForEntries] fields VALUES = and biodb.DEBUG[2025-04-21 19:22:11.206][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:11.208][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:11.210][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:22:11.212][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:11.213][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:22:11.215][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:22:11.216][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:22:11.217][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:22:11.218][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:22:11.220][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:22:11.221][private$doSearchForEntries] Total number of IDs = 2 biodb.DEBUG[2025-04-21 19:22:11.223][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2025-04-21 19:22:11.224][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2025-04-21 19:22:11.227][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:11.228][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2025-04-21 19:22:11.231][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001". biodb.TRACE[2025-04-21 19:22:11.233][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-04-21 19:22:11.235][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml". biodb.DEBUG[2025-04-21 19:22:11.237][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2025-04-21 19:22:11.238][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:22:11.240][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:22:11.250][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:11.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.263][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:22:11.269][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.271][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.272][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.274][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.281][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.282][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.283][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.284][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.286][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.291][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:11.292][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:11.294][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.295][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.297][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:11.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:11.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.302][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:11.304][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:11.305][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.306][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:11.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:11.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.313][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.315][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.316][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.318][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.325][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.326][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.327][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.329][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.336][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.338][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.339][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.341][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.342][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.348][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.349][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.351][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.352][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.353][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.359][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.360][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.362][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.363][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.364][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.370][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.393][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.395][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.396][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.404][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:11.405][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:11.407][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.409][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:11.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:11.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.424][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:11.426][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:11.427][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.428][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:11.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:11.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.435][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.437][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.438][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.439][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.446][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.447][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.449][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.452][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.459][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.460][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.462][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.463][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.470][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.471][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.473][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.474][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.476][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.482][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:11.483][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:11.485][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.486][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:11.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:11.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.493][ef$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:22:11.495][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.496][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.498][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.500][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:22:11.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.523][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:11.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:11.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.529][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:11.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:11.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.534][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:11.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:11.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.539][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:11.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:11.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.544][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:11.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:11.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.549][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:11.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:11.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:11.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:11.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:11.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.622][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.627][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:11.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.637][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:11.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.648][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.653][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.658][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:11.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:11.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:11.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:11.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:11.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:11.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:11.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:11.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:11.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:11.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:11.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:11.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.720][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.727][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.732][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:11.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:11.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.766][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.771][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:11.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.783][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.788][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.793][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:11.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.799][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:11.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:11.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:11.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:11.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.809][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:11.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:11.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.815][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:22:11.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:11.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.835][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:22:11.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:11.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:11.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:11.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.877][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:11.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:11.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.893][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:11.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:11.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:11.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:11.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:11.946][self$createEntryFromContent] Accession numbers: HMDB0000001. biodb.TRACE[2025-04-21 19:22:11.947][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.953][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.958][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:11.964][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:11.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:11.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:11.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:11.969][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:22:11.970][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:22:11.971][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:11.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:11.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:11.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:11.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:11.984][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:11.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:11.986][private$loadEntries] Creating entries from ids [1]: "HMDB0000002". biodb.DEBUG[2025-04-21 19:22:11.988][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2025-04-21 19:22:11.990][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:11.992][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2025-04-21 19:22:11.995][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002". biodb.TRACE[2025-04-21 19:22:11.997][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-04-21 19:22:11.999][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml". biodb.DEBUG[2025-04-21 19:22:12.001][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2025-04-21 19:22:12.003][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2025-04-21 19:22:12.004][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2025-04-21 19:22:12.006][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:12.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:12.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:12.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:12.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:12.019][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:12.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:22:12.024][ef$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.026][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.035][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.037][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.045][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.047][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.048][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.049][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.051][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.056][ef$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:12.057][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:12.059][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.060][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.061][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:12.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:12.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.067][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:12.068][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:12.069][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.070][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.072][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:12.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.078][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.079][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.080][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.082][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.089][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.090][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.091][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.092][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.098][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.099][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.100][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.101][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.103][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.108][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.110][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.111][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.112][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.114][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.120][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.121][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.122][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.123][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.125][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.130][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.131][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.132][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.133][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.140][ef$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:12.141][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:12.142][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.143][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.145][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:12.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:12.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.150][ef$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:12.152][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:12.153][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.154][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.161][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.162][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.163][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.165][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.179][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.181][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.183][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.184][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.192][ef$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.193][ef$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.195][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.196][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.203][ef$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.205][ef$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.206][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.207][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.208][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.214][ef$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:12.215][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:12.216][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.217][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.219][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:12.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:12.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.224][ef$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:22:12.225][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.227][ef$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.228][ef$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.230][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2025-04-21 19:22:12.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.250][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:12.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:12.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.254][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:12.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:12.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.259][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-04-21 19:22:12.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-04-21 19:22:12.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.264][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:12.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:12.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.270][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:12.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:12.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.275][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-04-21 19:22:12.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-04-21 19:22:12.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-04-21 19:22:12.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2025-04-21 19:22:12.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2025-04-21 19:22:12.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.346][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2025-04-21 19:22:12.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.351][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2025-04-21 19:22:12.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.365][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.371][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.376][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:12.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:12.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:12.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-04-21 19:22:12.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-04-21 19:22:12.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:12.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:12.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:12.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:12.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-04-21 19:22:12.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-04-21 19:22:12.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.431][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.436][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.442][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-04-21 19:22:12.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-04-21 19:22:12.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.488][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.493][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.498][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2025-04-21 19:22:12.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.503][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.525][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.530][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2025-04-21 19:22:12.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.534][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:12.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:12.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.540][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:12.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:12.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-04-21 19:22:12.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-04-21 19:22:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.550][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:22:12.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-04-21 19:22:12.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.578][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2025-04-21 19:22:12.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-04-21 19:22:12.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-04-21 19:22:12.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-04-21 19:22:12.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.610][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:12.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.615][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:12.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:12.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.632][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:12.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2025-04-21 19:22:12.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-04-21 19:22:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-04-21 19:22:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:12.670][self$createEntryFromContent] Accession numbers: HMDB0000002. biodb.TRACE[2025-04-21 19:22:12.671][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.676][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.680][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.686][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:12.691][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:22:12.692][private$doSearchForEntries] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:22:12.694][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:12.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:12.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:12.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:12.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:12.708][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:12.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:12.716][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2025-04-21 19:22:12.718][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular") biodb.DEBUG[2025-04-21 19:22:12.719][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular") biodb.DEBUG[2025-04-21 19:22:12.722][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:12.724][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:12.726][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:22:12.728][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:12.729][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:22:12.731][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:22:12.733][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:22:12.734][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:22:12.735][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:22:12.737][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:22:12.738][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2025-04-21 19:22:12.740][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.758][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.763][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.768][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:12.788][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:22:12.790][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:22:12.792][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:12.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:12.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:12.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:12.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:12.805][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:12.807][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.TRACE[2025-04-21 19:22:12.809][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.813][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.819][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.824][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.839][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:12.844][private$doSearchForEntries] MATCHED = FALSE biodb.DEBUG[2025-04-21 19:22:12.845][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:22:12.846][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:12.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:12.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:12.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:12.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:12.859][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:12.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-04-21 19:22:12.868][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2025-04-21 19:22:12.875][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes") biodb.DEBUG[2025-04-21 19:22:12.876][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes") biodb.DEBUG[2025-04-21 19:22:12.879][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:12.881][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:12.883][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2025-04-21 19:22:12.885][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2025-04-21 19:22:12.886][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2025-04-21 19:22:12.889][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2025-04-21 19:22:12.895][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2025-04-21 19:22:12.897][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2025-04-21 19:22:12.899][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2025-04-21 19:22:12.902][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2025-04-21 19:22:12.908][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2025-04-21 19:22:12.910][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.927][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.932][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.938][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.943][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.948][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.954][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:12.958][private$doSearchForEntries] MATCHED = FALSE biodb.DEBUG[2025-04-21 19:22:12.967][private$doSearchForEntries] COUNT IDS = 0 biodb.DEBUG[2025-04-21 19:22:12.968][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:12.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:12.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:12.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:12.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:12.982][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:12.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-04-21 19:22:12.985][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.990][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:12.995][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:12.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:12.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:12.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:13.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:13.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:13.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:13.006][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:13.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:13.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:13.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:13.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:13.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:13.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-04-21 19:22:13.015][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2025-04-21 19:22:13.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2025-04-21 19:22:13.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-04-21 19:22:13.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-04-21 19:22:13.020][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2025-04-21 19:22:13.021][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2025-04-21 19:22:13.023][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-04-21 19:22:13.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:13.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:13.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:13.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:13.035][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:13.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-04-21 19:22:13.048][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-04-21 19:22:13.050][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2025-04-21 19:22:13.052][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2025-04-21 19:22:13.054][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-04-21 19:22:13.055][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-04-21 19:22:13.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-04-21 19:22:13.058][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-04-21 19:22:13.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-04-21 19:22:13.061][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-04-21 19:22:13.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ] > > proc.time() user system elapsed 11.157 0.723 20.733