Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:36:19 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 202/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbHmdb 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.10.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbHmdb_1.10.0.tar.gz |
StartedAt: 2024-05-03 21:09:16 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 21:10:08 -0400 (Fri, 03 May 2024) |
EllapsedTime: 51.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: biodbHmdb.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbHmdb_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘biodbHmdb/DESCRIPTION’ ... OK * this is package ‘biodbHmdb’ version ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbHmdb’ can be installed ... WARNING Found the following significant warnings: EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder] EntryMaker.hpp:22:14: warning: ‘bool EntryMaker::closed’ [-Wreorder] EntryMaker.cpp:5:1: warning: when initialized here [-Wreorder] See ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck/00check.log’ for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c EntryMaker.cpp -o EntryMaker.o In file included from EntryMaker.cpp:1: EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’: EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder] 23 | TagDetector accession_tag; | ^~~~~~~~~~~~~ EntryMaker.hpp:22:14: warning: ‘bool EntryMaker::closed’ [-Wreorder] 22 | bool closed; | ^~~~~~ EntryMaker.cpp:5:1: warning: when initialized here [-Wreorder] 5 | EntryMaker::EntryMaker() : | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c FileEntryMaker.cpp -o FileEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c TagDetector.cpp -o TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c XmlSplitter.cpp -o XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-TagDetector.cpp -o test-100-TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbHmdb) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbHmdb") biodb.INFO [2024-05-03 21:09:50.623][biodb::testContext] biodb.INFO [2024-05-03 21:09:50.625][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:50.626][biodb::testContext] Test context - Tests of independent functions biodb.INFO [2024-05-03 21:09:50.627][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:50.628][biodb::testContext] biodb.INFO [2024-05-03 21:09:50.629][biodb::testThat] biodb.INFO [2024-05-03 21:09:50.630][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. "). biodb.INFO [2024-05-03 21:09:50.631][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:50.632][biodb::testThat] biodb.INFO [2024-05-03 21:09:50.735][biodb::testContext] biodb.INFO [2024-05-03 21:09:50.737][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:50.738][biodb::testContext] Test context - Generic tests biodb.INFO [2024-05-03 21:09:50.739][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:50.740][biodb::testContext] biodb.INFO [2024-05-03 21:09:50.749][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:09:50.751][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-03 21:09:50.759][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:50.760][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-03 21:09:50.774][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-03 21:09:50.775][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.778][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-03 21:09:50.798][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-03 21:09:50.799][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.802][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-03 21:09:50.803][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-03 21:09:50.804][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.807][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-03 21:09:50.808][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-03 21:09:50.809][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-03 21:09:50.810][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.813][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-03 21:09:50.814][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-03 21:09:50.815][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-03 21:09:50.816][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.818][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-03 21:09:50.819][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-03 21:09:50.820][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.823][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-03 21:09:50.824][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-03 21:09:50.825][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-03 21:09:50.826][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.829][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-03 21:09:50.830][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-03 21:09:50.831][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.833][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-03 21:09:50.834][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-03 21:09:50.835][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-03 21:09:50.836][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.839][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:09:50.840][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-03 21:09:50.841][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-03 21:09:50.842][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-03 21:09:50.843][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-03 21:09:50.844][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-03 21:09:50.845][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.848][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-03 21:09:50.849][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-03 21:09:50.850][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.852][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-03 21:09:50.853][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-03 21:09:50.854][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.857][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-03 21:09:50.858][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-03 21:09:50.859][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.861][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-03 21:09:50.862][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-03 21:09:50.863][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.866][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-03 21:09:50.867][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-03 21:09:50.868][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.871][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:09:50.872][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-03 21:09:50.875][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-03 21:09:50.876][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.879][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-03 21:09:50.880][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-03 21:09:50.881][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-03 21:09:50.881][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:50.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:50.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:50.887][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-03 21:09:50.919][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.934][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-03 21:09:50.935][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.936][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:50.937][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.938][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:50.939][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.940][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:50.941][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:09:50.942][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:50.948][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.949][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-03 21:09:50.950][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:50.951][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:50.951][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.952][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:50.952][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:09:50.952][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:09:50.952][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:09:50.952][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:09:50.953][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:50.954][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:50.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:50.956][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:50.957][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:50.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:50.958][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:50.959][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:50.960][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:50.961][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:50.962][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.963][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:50.964][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-03 21:09:50.965][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.966][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:09:50.967][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.968][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:50.969][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:50.971][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.972][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:50.973][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:09:50.974][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:50.975][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.976][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-03 21:09:50.976][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:50.977][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:50.978][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.979][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:50.979][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:09:50.979][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:09:50.979][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:09:50.979][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:09:50.980][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:50.981][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:50.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:50.983][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:50.984][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:50.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:50.985][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:50.986][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:50.987][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:50.988][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:50.989][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.990][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:50.991][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-03 21:09:50.993][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.994][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-03 21:09:50.995][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.995][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:50.996][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:50.997][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:50.998][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:50.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:51.000][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:09:51.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:51.002][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.003][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-03 21:09:51.004][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:51.005][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.005][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.006][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.007][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:51.008][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:51.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:51.010][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:51.011][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:51.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:51.013][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:51.013][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.014][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:51.015][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:51.016][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.017][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.018][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-03 21:09:51.020][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.021][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:09:51.022][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.022][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:51.023][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:51.025][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:51.027][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:09:51.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:51.029][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.030][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-03 21:09:51.031][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:51.032][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.033][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.034][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.034][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:51.035][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:51.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:51.037][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:51.038][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:51.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:51.040][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:51.041][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.042][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:51.042][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:51.043][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.044][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.048][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:51.049][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.050][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[2024-05-03 21:09:51.051][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.055][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.059][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.062][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". biodb.DEBUG[2024-05-03 21:09:51.063][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.067][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[2024-05-03 21:09:51.067][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.072][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.076][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.080][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.084][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.089][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.093][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.096][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[2024-05-03 21:09:51.097][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.101][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.105][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[2024-05-03 21:09:51.105][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.119][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.123][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.127][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-03 21:09:51.132][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-03 21:09:51.134][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-03 21:09:51.135][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-03 21:09:51.136][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-03 21:09:51.138][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:09:51.139][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-03 21:09:51.140][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-03 21:09:51.141][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-03 21:09:51.143][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:09:51.144][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:09:51.145][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-03 21:09:51.147][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-03 21:09:51.148][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-03 21:09:51.149][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-03 21:09:51.151][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:09:51.152][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-03 21:09:51.153][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-03 21:09:51.154][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-03 21:09:51.156][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-03 21:09:51.157][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-03 21:09:51.158][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-03 21:09:51.160][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-03 21:09:51.161][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-03 21:09:51.162][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-03 21:09:51.163][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-03 21:09:51.165][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-03 21:09:51.166][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-03 21:09:51.167][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-03 21:09:51.169][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-03 21:09:51.170][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-03 21:09:51.171][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-03 21:09:51.172][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-03 21:09:51.174][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-03 21:09:51.175][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-03 21:09:51.176][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-03 21:09:51.178][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-03 21:09:51.179][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-03 21:09:51.180][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-03 21:09:51.182][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-03 21:09:51.183][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-03 21:09:51.184][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-03 21:09:51.186][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-03 21:09:51.187][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-03 21:09:51.188][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-03 21:09:51.190][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-03 21:09:51.191][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-03 21:09:51.192][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-03 21:09:51.194][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-03 21:09:51.195][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-03 21:09:51.196][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-03 21:09:51.198][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-03 21:09:51.199][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-03 21:09:51.200][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-03 21:09:51.201][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-03 21:09:51.203][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-03 21:09:51.204][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-03 21:09:51.205][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-03 21:09:51.207][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-03 21:09:51.208][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-03 21:09:51.209][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-03 21:09:51.211][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-03 21:09:51.212][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-03 21:09:51.213][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-03 21:09:51.214][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-03 21:09:51.216][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-03 21:09:51.217][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-03 21:09:51.218][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-03 21:09:51.220][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-03 21:09:51.221][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-03 21:09:51.222][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-03 21:09:51.224][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-03 21:09:51.225][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-03 21:09:51.226][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-03 21:09:51.227][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-03 21:09:51.229][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-03 21:09:51.230][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-03 21:09:51.231][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-03 21:09:51.233][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-03 21:09:51.234][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-03 21:09:51.235][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-03 21:09:51.237][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-03 21:09:51.238][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-03 21:09:51.244][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-03 21:09:51.245][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:09:51.249][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:51.249][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.251][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.257][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.263][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.269][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.275][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.287][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.293][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.299][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.305][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.311][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.316][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[2024-05-03 21:09:51.317][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.322][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[2024-05-03 21:09:51.323][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.329][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.335][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.341][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.347][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.352][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[2024-05-03 21:09:51.353][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.359][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:51.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:51.366][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/definitions.yml". biodb.DEBUG[2024-05-03 21:09:51.375][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:51.378][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.379][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-03 21:09:51.380][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.381][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:51.382][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.383][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2024-05-03 21:09:51.384][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.385][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:51.386][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-03 21:09:51.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:51.388][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.389][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2024-05-03 21:09:51.390][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2024-05-03 21:09:51.391][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2024-05-03 21:09:51.392][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-03 21:09:51.393][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:51.393][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2024-05-03 21:09:51.393][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2024-05-03 21:09:51.394][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-03 21:09:51.395][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:51.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:51.397][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:51.397][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:51.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:51.399][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:51.400][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-03 21:09:51.400][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2024-05-03 21:09:51.401][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:51.402][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:51.403][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:51.404][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:51.410][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2024-05-03 21:09:51.411][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:09:51.413][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:09:51.414][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:09:51.416][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:09:51.440][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:51.441][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2024-05-03 21:09:51.445][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:51.450][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:51.454][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:51.455][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:51.457][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2024-05-03 21:09:51.458][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.DEBUG[2024-05-03 21:09:51.459][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-03 21:09:51.459][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip". biodb.DEBUG[2024-05-03 21:09:51.498][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:51.498][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:51.499][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler. biodb.DEBUG[2024-05-03 21:09:51.500][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize". biodb.DEBUG[2024-05-03 21:09:51.501][self$registerConnector] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:51.517][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:51.519][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:51.520][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:51.521][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:51.522][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:51.523][self$setFrequency] t=1.000000, n=3.000000 biodb.INFO [2024-05-03 21:09:51.531][biodb::testThat] biodb.INFO [2024-05-03 21:09:51.532][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-03 21:09:51.533][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:51.534][biodb::testThat] biodb.TRACE[2024-05-03 21:09:51.539][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml". biodb.DEBUG[2024-05-03 21:09:51.541][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:09:51.544][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:09:51.553][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:09:51.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:51.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:51.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:51.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:51.561][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:51.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:09:51.573][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:51.575][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:51.575][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.576][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:51.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:51.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.593][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.594][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.595][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.596][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.621][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.625][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:51.626][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:51.627][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.628][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.630][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:51.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:51.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.633][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:51.634][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:51.635][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.636][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.637][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:51.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.641][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.642][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.643][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.644][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.656][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.657][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.658][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.659][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.664][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.665][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.666][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.666][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.668][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.672][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.673][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.673][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.674][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.680][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.681][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.682][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.683][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.688][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.689][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.690][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.691][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.696][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:51.697][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:51.698][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.699][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:51.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:51.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.704][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:51.705][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:51.706][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.707][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:51.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:51.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.712][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:51.713][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:51.714][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.715][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:51.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:51.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.720][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.721][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.722][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.723][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.728][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:51.729][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:51.730][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.731][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:51.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:51.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.736][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:51.737][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:51.738][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.739][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.740][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:51.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:51.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.744][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:51.745][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:51.746][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.747][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.748][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:51.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:51.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.752][ef$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:51.753][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.754][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.755][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.757][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:51.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:51.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:51.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:51.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:51.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:51.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.809][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:51.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:51.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.813][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:51.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:51.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.817][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:51.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:51.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.821][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:51.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:51.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.824][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:51.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:51.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:51.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:51.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:51.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:51.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:51.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.889][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:51.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:51.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.893][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:51.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:51.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.897][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:51.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:51.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:51.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:51.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:51.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:51.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.908][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:51.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:51.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:51.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:51.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:51.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:51.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:51.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:51.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:51.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:51.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:51.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:51.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:51.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:51.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.938][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.942][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:51.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:51.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:51.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:51.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:51.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:51.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:51.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:51.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.976][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.980][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:51.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.983][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.987][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.991][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:51.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.995][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:51.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:51.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:51.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:51.999][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.006][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:09:52.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.021][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:09:52.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.059][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.067][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.071][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.078][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:52.104][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001. biodb.TRACE[2024-05-03 21:09:52.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:09:52.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:09:52.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:09:52.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:09:52.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:09:52.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:09:52.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.118][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:09:52.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:09:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.144][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.175][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.182][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:52.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.205][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.206][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.211][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.212][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.224][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.228][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.232][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.235][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.236][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.237][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.238][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.239][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.261][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.262][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.263][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.264][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.287][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.288][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.289][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.290][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.291][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.313][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.314][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.315][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.316][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.327][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.331][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.335][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.339][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.339][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.340][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.341][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.342][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.368][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.369][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.370][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.371][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.382][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:52.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.386][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:52.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:52.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.390][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:52.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:52.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.394][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:52.395][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:52.395][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.396][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.397][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:52.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:52.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.420][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.421][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.422][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.422][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.423][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.434][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.438][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.442][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.446][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.447][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.448][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.449][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.450][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.472][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.473][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.474][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.475][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.503][ef$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.504][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.504][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.505][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.528][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.529][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.530][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.531][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.554][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.555][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.556][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.557][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.572][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.580][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.581][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.582][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.582][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.583][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.605][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.606][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.607][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.608][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.636][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.637][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.638][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.639][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.651][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.659][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.662][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.663][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.664][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.665][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.666][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.677][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.678][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.679][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.680][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.684][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.686][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.686][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.687][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.692][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.693][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.694][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.695][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.699][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.700][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.701][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.702][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.706][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.707][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.708][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.709][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.713][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.714][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.715][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.716][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.720][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.721][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.722][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.723][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.727][ef$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.728][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:52.729][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.730][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.734][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:52.735][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:52.736][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.737][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.741][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.742][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.743][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.744][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.748][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.749][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.750][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.751][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.755][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.756][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.761][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.762][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.766][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.767][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.768][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.769][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.773][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.774][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.775][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.776][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.780][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:52.781][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:52.782][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.783][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.787][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.788][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.789][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.790][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.794][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.795][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.796][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.797][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.801][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:52.803][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:52.803][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.804][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:09:52.811][biodb::testThat] biodb.INFO [2024-05-03 21:09:52.812][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-03 21:09:52.813][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:52.814][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:52.827][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2024-05-03 21:09:52.835][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-03 21:09:52.840][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:52.841][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2024-05-03 21:09:52.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001". biodb.TRACE[2024-05-03 21:09:52.844][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:09:52.847][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml". biodb.DEBUG[2024-05-03 21:09:52.848][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:09:52.870][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:09:52.872][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:09:52.873][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:09:52.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:52.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:52.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:52.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:52.881][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:52.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:09:52.885][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.886][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.887][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.888][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:52.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:52.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.893][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.894][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.901][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.902][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:52.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.907][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.908][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.909][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.910][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.911][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:52.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:52.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.915][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.916][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.917][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.918][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.919][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.923][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.924][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.925][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.926][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:52.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.931][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.932][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.933][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.934][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:52.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.939][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.940][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.941][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.942][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.943][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:52.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.947][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.948][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.949][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.949][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.951][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:52.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.955][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.956][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.956][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.957][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:52.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.962][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.963][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.964][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.965][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.967][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:52.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.970][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.971][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.972][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.973][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:52.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:52.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.978][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.979][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.980][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.981][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:52.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:52.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.986][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.987][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.988][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.989][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:52.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:52.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.994][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.995][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.995][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:52.996][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:52.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:52.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.001][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.002][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.003][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.004][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.009][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.010][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.011][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.012][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.013][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.017][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:53.017][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:53.018][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.019][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:53.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:53.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.024][ef$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:53.025][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.026][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.027][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.028][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:53.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:53.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.054][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:53.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:53.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.058][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:53.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:53.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.062][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:53.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:53.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.065][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:53.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:53.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:53.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:53.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:53.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:53.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:53.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:53.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:53.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:53.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:53.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:53.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:53.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:53.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.095][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:53.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:53.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:53.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:53.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:53.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:53.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.106][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:53.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:53.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:53.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:53.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.113][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.117][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:53.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.124][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:53.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.139][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:53.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:53.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:53.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:53.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:53.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:53.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:53.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:53.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:53.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:53.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:53.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:53.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.172][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:53.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:53.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.176][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:53.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:53.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.179][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:53.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:53.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:53.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:53.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:53.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:53.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:53.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:53.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.205][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:53.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:53.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:53.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:53.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.213][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:53.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:53.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.216][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.220][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.224][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.227][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:53.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:53.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.231][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:53.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:53.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.235][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:53.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:53.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.239][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:09:53.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:53.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:53.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:53.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.253][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:09:53.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:53.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.276][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:53.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:53.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.280][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:53.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:53.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.291][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:53.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:53.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:53.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.317][self$createEntryFromContent] Accession numbers: HMDB0000001. biodb.TRACE[2024-05-03 21:09:53.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-03 21:09:53.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-03 21:09:53.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-03 21:09:53.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-03 21:09:53.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-03 21:09:53.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-03 21:09:53.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:09:53.335][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.336][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-03 21:09:53.337][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:53.338][biodb::testThat] biodb.TRACE[2024-05-03 21:09:53.341][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.342][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.343][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.344][ef$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.345][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name". biodb.TRACE[2024-05-03 21:09:53.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.382][function(conn, opt)] With value "1-Methylhistidine". biodb.DEBUG[2024-05-03 21:09:53.384][private$doSearchForEntries] fields NAMES = name biodb.DEBUG[2024-05-03 21:09:53.384][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2024-05-03 21:09:53.385][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2024-05-03 21:09:53.387][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.388][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.390][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:53.391][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.392][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:53.393][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:53.394][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:53.395][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:53.396][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:09:53.397][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:09:53.398][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2024-05-03 21:09:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.419][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:09:53.420][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:09:53.421][function(conn, opt)] With found IDs [1]: "HMDB0000001". biodb.TRACE[2024-05-03 21:09:53.430][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.431][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.432][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.433][ef$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.434][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description". biodb.TRACE[2024-05-03 21:09:53.444][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.448][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.451][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.457][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.". biodb.DEBUG[2024-05-03 21:09:53.507][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2024-05-03 21:09:53.508][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat. biodb.DEBUG[2024-05-03 21:09:53.509][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat. biodb.DEBUG[2024-05-03 21:09:53.522][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.528][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.529][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:53.531][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.532][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:53.546][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:53.547][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:53.548][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:53.549][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:09:53.550][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:09:53.551][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2024-05-03 21:09:53.552][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.556][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.560][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:53.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.567][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:09:53.568][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:09:53.569][function(conn, opt)] With found IDs [1]: "HMDB0000001". biodb.TRACE[2024-05-03 21:09:53.579][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.581][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.582][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.582][ef$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.584][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions". biodb.TRACE[2024-05-03 21:09:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.601][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.607][function(conn, opt)] With value "HMDB00001". biodb.DEBUG[2024-05-03 21:09:53.609][private$doSearchForEntries] fields NAMES = secondary.accessions biodb.DEBUG[2024-05-03 21:09:53.610][private$doSearchForEntries] fields VALUES = HMDB00001 biodb.DEBUG[2024-05-03 21:09:53.611][private$doSearchForEntries] fields VALUES = HMDB00001 biodb.DEBUG[2024-05-03 21:09:53.612][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.613][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.615][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:53.616][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.617][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:53.618][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:53.619][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:53.620][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:53.621][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:09:53.622][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:09:53.623][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2024-05-03 21:09:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.628][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.632][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.636][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:53.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.640][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:09:53.641][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:09:53.641][function(conn, opt)] With found IDs [1]: "HMDB0000001". biodb.INFO [2024-05-03 21:09:53.659][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.661][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-03 21:09:53.662][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:53.662][biodb::testThat] biodb.TRACE[2024-05-03 21:09:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.694][private$doSearchForEntries] fields NAMES = name biodb.DEBUG[2024-05-03 21:09:53.696][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2024-05-03 21:09:53.697][private$doSearchForEntries] fields VALUES = 1-Methylhistidine biodb.DEBUG[2024-05-03 21:09:53.698][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.700][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.701][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:53.702][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:53.703][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:53.705][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:53.706][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:53.707][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:53.708][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:09:53.709][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:09:53.709][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2024-05-03 21:09:53.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:53.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:53.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:53.727][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:09:53.728][private$doSearchForEntries] COUNT IDS = 1 biodb.INFO [2024-05-03 21:09:53.741][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.743][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-03 21:09:53.744][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:53.744][biodb::testThat] biodb.TRACE[2024-05-03 21:09:53.764][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:09:53.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:09:53.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.776][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:09:53.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:09:53.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.826][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:09:53.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:09:53.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:09:53.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:53.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:09:53.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:09:53.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:53.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:09:53.843][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.843][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-03 21:09:53.844][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:53.845][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.852][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.853][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-03 21:09:53.854][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:53.855][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.862][biodb::testThat] biodb.INFO [2024-05-03 21:09:53.863][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-03 21:09:53.864][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:53.865][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:53.868][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001". biodb.DEBUG[2024-05-03 21:09:56.616][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001. biodb.INFO [2024-05-03 21:09:56.686][biodb::testThat] biodb.INFO [2024-05-03 21:09:56.688][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-03 21:09:56.689][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:56.690][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:57.488][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png. biodb.TRACE[2024-05-03 21:09:57.512][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:57.514][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:57.515][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.517][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.519][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:57.520][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:57.522][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.523][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.525][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:57.526][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:57.528][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.529][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:09:57.532][biodb::testThat] biodb.INFO [2024-05-03 21:09:57.533][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2024-05-03 21:09:57.535][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:57.536][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:57.539][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2024-05-03 21:09:57.634][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-03 21:09:57.636][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.637][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2024-05-03 21:09:57.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA". biodb.TRACE[2024-05-03 21:09:57.656][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-03 21:09:57.657][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-03 21:09:57.658][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:09:57.660][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.661][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:09:57.662][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:09:57.664][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:09:57.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:57.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:57.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:57.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:57.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:09:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.679][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:57.710][self$createEntryFromContent] Accession numbers: NA. biodb.DEBUG[2024-05-03 21:09:57.711][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2024-05-03 21:09:57.726][biodb::testThat] biodb.INFO [2024-05-03 21:09:57.727][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2024-05-03 21:09:57.728][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:57.729][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:57.737][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001" biodb.DEBUG[2024-05-03 21:09:57.738][private$loadEntries] Creating entries from ids [1]: "WRONGB". biodb.DEBUG[2024-05-03 21:09:57.739][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-03 21:09:57.740][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.742][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2024-05-03 21:09:57.743][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB". biodb.TRACE[2024-05-03 21:09:57.745][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-03 21:09:57.746][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-03 21:09:57.747][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:09:57.748][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.749][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:09:57.750][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:09:57.752][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:09:57.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:57.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:57.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:57.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:57.760][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:09:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.767][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:57.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:57.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:57.827][self$createEntryFromContent] Accession numbers: NA. biodb.DEBUG[2024-05-03 21:09:57.827][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-03 21:09:57.828][function(conn, opt)] Entries: [2]: "NULL, <environment>" biodb.INFO [2024-05-03 21:09:57.840][biodb::testThat] biodb.INFO [2024-05-03 21:09:57.841][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2024-05-03 21:09:57.842][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:57.843][biodb::testThat] biodb.INFO [2024-05-03 21:09:57.862][biodb::testThat] biodb.INFO [2024-05-03 21:09:57.864][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2024-05-03 21:09:57.865][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:57.865][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:57.868][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.869][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.870][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:57.872][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.873][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:57.874][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:57.875][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:57.876][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:57.877][private$doGetEntryIds] COUNT IDS = 2 biodb.INFO [2024-05-03 21:09:57.884][biodb::testThat] biodb.INFO [2024-05-03 21:09:57.885][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2024-05-03 21:09:57.886][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:57.887][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:57.889][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.890][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.891][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:57.893][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:57.894][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:57.895][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:57.896][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:57.897][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:57.898][private$doGetEntryIds] COUNT IDS = 2 biodb.TRACE[2024-05-03 21:09:57.905][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:57.906][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:57.907][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.908][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.909][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:57.910][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:57.911][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.912][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:57.913][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:57.914][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:57.915][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:57.916][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:09:57.917][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-03 21:09:57.918][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2024-05-03 21:09:57.931][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2024-05-03 21:09:57.932][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-03 21:09:57.933][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:57.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:57.935][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:57.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:57.936][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-03 21:09:57.941][biodb::testContext] biodb.INFO [2024-05-03 21:09:57.942][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:57.943][biodb::testContext] Test context - Test retrieval of entries biodb.INFO [2024-05-03 21:09:57.944][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:57.944][biodb::testContext] biodb.INFO [2024-05-03 21:09:57.948][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:09:57.950][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-03 21:09:57.953][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:57.954][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-03 21:09:57.955][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-03 21:09:57.956][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:57.959][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-03 21:09:57.960][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-03 21:09:57.961][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:57.963][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-03 21:09:57.964][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-03 21:09:57.965][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:57.968][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-03 21:09:57.972][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-03 21:09:57.974][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-03 21:09:57.976][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:57.979][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-03 21:09:57.980][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-03 21:09:57.982][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-03 21:09:57.983][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:57.986][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-03 21:09:57.987][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-03 21:09:57.988][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.990][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[2024-05-03 21:09:57.991][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-03 21:09:57.992][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-03 21:09:57.993][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-03 21:09:57.994][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:57.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:57.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:57.997][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-03 21:09:57.998][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-03 21:09:57.999][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.003][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-03 21:09:58.004][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-03 21:09:58.006][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-03 21:09:58.007][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.010][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:09:58.011][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-03 21:09:58.012][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-03 21:09:58.013][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-03 21:09:58.014][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-03 21:09:58.015][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-03 21:09:58.016][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.020][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-03 21:09:58.021][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-03 21:09:58.022][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.025][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-03 21:09:58.026][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-03 21:09:58.027][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.030][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-03 21:09:58.031][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-03 21:09:58.032][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.036][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-03 21:09:58.037][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-03 21:09:58.038][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.041][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-03 21:09:58.042][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-03 21:09:58.043][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.047][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:09:58.048][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-03 21:09:58.070][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-03 21:09:58.072][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.075][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-03 21:09:58.076][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-03 21:09:58.077][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-03 21:09:58.078][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.081][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-03 21:09:58.083][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.084][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-03 21:09:58.085][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.086][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:58.087][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:58.089][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:58.091][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:09:58.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:58.093][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.094][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-03 21:09:58.096][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:58.097][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.098][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.099][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:58.099][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:09:58.099][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:09:58.099][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:09:58.099][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:09:58.100][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:58.101][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.103][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:58.104][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.106][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:58.107][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.108][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:58.109][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:58.110][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.111][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.112][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-03 21:09:58.114][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.115][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:09:58.115][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.116][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:58.117][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:58.119][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:58.121][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:09:58.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:58.123][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.124][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-03 21:09:58.125][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:58.126][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.127][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.128][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:58.128][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:09:58.128][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:09:58.128][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:09:58.128][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:09:58.129][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:58.130][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.132][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:58.132][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.134][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:58.135][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.136][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:58.137][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:58.138][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.139][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.141][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-03 21:09:58.142][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.143][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-03 21:09:58.144][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.145][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:58.146][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:58.148][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.149][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:58.150][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:09:58.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:58.152][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.153][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-03 21:09:58.154][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:58.155][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.156][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.156][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.157][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:58.158][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.160][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:58.161][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.163][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:58.164][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.165][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:58.166][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:58.166][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.167][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.169][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-03 21:09:58.170][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.171][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:09:58.172][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.173][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:58.179][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:58.181][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.182][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:58.183][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:09:58.184][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:58.185][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.186][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-03 21:09:58.186][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:58.187][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.188][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.189][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.190][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:58.191][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.193][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:58.194][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.196][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:58.196][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.197][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:58.198][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:58.199][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.200][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.201][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:58.202][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.204][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.208][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.213][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.217][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.221][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.225][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.229][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.234][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.238][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.242][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.246][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.251][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.255][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.259][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.263][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.267][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.272][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.276][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-03 21:09:58.282][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-03 21:09:58.283][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-03 21:09:58.285][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-03 21:09:58.286][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-03 21:09:58.287][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:09:58.289][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-03 21:09:58.290][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-03 21:09:58.291][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-03 21:09:58.293][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:09:58.294][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:09:58.295][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-03 21:09:58.297][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-03 21:09:58.298][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-03 21:09:58.299][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-03 21:09:58.300][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:09:58.302][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-03 21:09:58.303][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-03 21:09:58.304][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-03 21:09:58.306][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-03 21:09:58.307][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-03 21:09:58.308][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-03 21:09:58.310][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-03 21:09:58.311][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-03 21:09:58.312][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-03 21:09:58.313][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-03 21:09:58.315][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-03 21:09:58.316][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-03 21:09:58.317][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-03 21:09:58.319][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-03 21:09:58.320][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-03 21:09:58.321][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-03 21:09:58.323][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-03 21:09:58.324][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-03 21:09:58.325][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-03 21:09:58.326][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-03 21:09:58.328][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-03 21:09:58.329][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-03 21:09:58.330][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-03 21:09:58.332][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-03 21:09:58.333][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-03 21:09:58.334][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-03 21:09:58.336][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-03 21:09:58.337][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-03 21:09:58.338][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-03 21:09:58.340][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-03 21:09:58.341][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-03 21:09:58.343][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-03 21:09:58.344][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-03 21:09:58.345][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-03 21:09:58.346][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-03 21:09:58.348][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-03 21:09:58.349][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-03 21:09:58.350][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-03 21:09:58.352][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-03 21:09:58.353][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-03 21:09:58.354][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-03 21:09:58.356][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-03 21:09:58.357][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-03 21:09:58.358][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-03 21:09:58.360][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-03 21:09:58.361][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-03 21:09:58.362][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-03 21:09:58.364][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-03 21:09:58.365][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-03 21:09:58.366][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-03 21:09:58.367][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-03 21:09:58.369][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-03 21:09:58.370][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-03 21:09:58.371][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-03 21:09:58.373][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-03 21:09:58.374][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-03 21:09:58.375][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-03 21:09:58.382][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-03 21:09:58.383][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-03 21:09:58.385][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-03 21:09:58.386][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-03 21:09:58.387][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-03 21:09:58.388][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-03 21:09:58.390][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-03 21:09:58.391][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-03 21:09:58.392][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-03 21:09:58.394][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-03 21:09:58.395][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-03 21:09:58.397][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:09:58.398][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:58.398][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.400][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.402][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.408][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.414][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.420][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.426][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.432][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.438][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.444][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.449][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.455][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.461][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.467][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.472][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[2024-05-03 21:09:58.473][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.483][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.489][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.495][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.501][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:58.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:58.507][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/definitions.yml". biodb.DEBUG[2024-05-03 21:09:58.509][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:58.511][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.512][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-03 21:09:58.513][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.513][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:58.514][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.515][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2024-05-03 21:09:58.516][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:58.518][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-03 21:09:58.519][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:58.520][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.521][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2024-05-03 21:09:58.522][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2024-05-03 21:09:58.523][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2024-05-03 21:09:58.524][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-03 21:09:58.525][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:58.525][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2024-05-03 21:09:58.525][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2024-05-03 21:09:58.526][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-03 21:09:58.527][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.528][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:58.529][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:58.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:58.531][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:58.532][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-03 21:09:58.532][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2024-05-03 21:09:58.533][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:58.534][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:58.535][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:58.536][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:58.537][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2024-05-03 21:09:58.538][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:09:58.540][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:09:58.541][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:09:58.543][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:09:58.546][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:58.547][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2024-05-03 21:09:58.548][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:58.549][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:58.550][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:58.551][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:58.552][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2024-05-03 21:09:58.553][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.DEBUG[2024-05-03 21:09:58.554][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-03 21:09:58.554][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip". biodb.DEBUG[2024-05-03 21:09:58.555][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:58.556][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:58.557][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler. biodb.DEBUG[2024-05-03 21:09:58.558][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize". biodb.DEBUG[2024-05-03 21:09:58.559][self$registerConnector] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:58.560][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:58.561][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:58.562][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:58.563][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:58.565][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:58.565][self$setFrequency] t=1.000000, n=3.000000 biodb.INFO [2024-05-03 21:09:58.567][biodb::testThat] biodb.INFO [2024-05-03 21:09:58.568][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. "). biodb.INFO [2024-05-03 21:09:58.569][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:58.570][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:58.574][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:58.575][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:58.576][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:58.578][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:58.578][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:58.580][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:58.585][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:58.586][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:58.587][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:09:58.590][conn$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.INFO [2024-05-03 21:09:58.595][biodb::testThat] biodb.INFO [2024-05-03 21:09:58.596][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. "). biodb.INFO [2024-05-03 21:09:58.597][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:58.598][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:58.600][private$loadEntries] Creating entries from ids [1]: "HMDB0000002". biodb.DEBUG[2024-05-03 21:09:58.601][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-03 21:09:58.602][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:58.603][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2024-05-03 21:09:58.605][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002". biodb.TRACE[2024-05-03 21:09:58.606][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:09:58.609][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml". biodb.DEBUG[2024-05-03 21:09:58.610][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:09:58.612][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:09:58.614][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:09:58.616][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:09:58.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:58.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:58.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:58.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:58.628][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:58.629][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.TRACE[2024-05-03 21:09:58.634][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:58.636][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:58.637][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.639][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:58.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:58.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.646][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:58.648][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:58.649][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.650][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.652][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:58.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:58.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.658][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:58.659][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:58.661][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.662][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.664][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:58.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:58.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.670][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:58.671][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:58.672][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.674][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.676][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:58.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:58.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.681][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.683][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.684][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.685][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.693][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.694][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.696][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.697][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.705][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.708][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.709][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.710][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.715][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:58.716][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:58.717][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.718][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.720][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:58.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:58.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.728][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.730][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.731][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.732][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.733][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.737][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.738][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.739][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.740][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.745][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:58.746][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:58.747][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.748][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:58.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:58.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.753][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:58.754][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:58.755][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.756][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:58.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:58.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.761][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:58.762][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:58.763][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.764][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:58.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:58.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.769][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.770][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.771][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.772][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.778][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:58.779][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:58.780][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.780][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.786][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:58.787][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:58.788][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.789][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.790][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:58.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:58.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.794][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:58.795][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:58.796][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.797][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:58.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:58.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.802][ef$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:58.803][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.804][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.805][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.806][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:58.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:58.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:58.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:58.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:58.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:58.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.822][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:58.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:58.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.826][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:58.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:58.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:58.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:58.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.839][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:58.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:58.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.843][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:58.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.846][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:58.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:58.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:58.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:58.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:58.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.886][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.890][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.894][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:58.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.898][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:58.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:58.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:58.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:58.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.917][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:58.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:58.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.921][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:58.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:58.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:58.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:58.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:58.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:58.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:58.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:58.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:58.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:58.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:58.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:58.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:58.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:58.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:58.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:58.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.968][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:58.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:58.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:58.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:58.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:58.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:58.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:58.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:58.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.996][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:58.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:58.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:58.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.003][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.007][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.015][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.019][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.023][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:59.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.027][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:59.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.031][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:09:59.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:59.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:59.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:09:59.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.075][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:59.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:59.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:59.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:59.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:09:59.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:09:59.114][self$createEntryFromContent] Accession numbers: HMDB0000002. biodb.TRACE[2024-05-03 21:09:59.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:09:59.132][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-03 21:09:59.133][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2024-05-03 21:09:59.134][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2024-05-03 21:09:59.135][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-03 21:09:59.136][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.138][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.140][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-03 21:09:59.144][biodb::testContext] biodb.INFO [2024-05-03 21:09:59.145][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:59.146][biodb::testContext] Test context - Test search of entries biodb.INFO [2024-05-03 21:09:59.152][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:09:59.153][biodb::testContext] biodb.INFO [2024-05-03 21:09:59.157][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:09:59.159][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-03 21:09:59.163][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:59.164][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-03 21:09:59.165][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-03 21:09:59.166][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.168][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-03 21:09:59.170][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-03 21:09:59.170][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.173][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-03 21:09:59.174][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-03 21:09:59.175][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.182][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-03 21:09:59.183][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-03 21:09:59.184][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-03 21:09:59.185][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.189][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-03 21:09:59.190][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-03 21:09:59.191][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-03 21:09:59.192][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.195][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-03 21:09:59.196][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-03 21:09:59.197][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.200][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-03 21:09:59.202][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-03 21:09:59.203][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-03 21:09:59.204][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.207][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-03 21:09:59.208][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-03 21:09:59.209][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.212][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-03 21:09:59.213][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-03 21:09:59.214][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-03 21:09:59.215][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.218][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:09:59.219][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-03 21:09:59.220][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-03 21:09:59.221][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-03 21:09:59.222][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-03 21:09:59.224][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-03 21:09:59.225][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.228][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-03 21:09:59.229][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-03 21:09:59.230][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.232][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[2024-05-03 21:09:59.233][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-03 21:09:59.234][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-03 21:09:59.235][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.238][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-03 21:09:59.239][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-03 21:09:59.240][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.243][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-03 21:09:59.244][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-03 21:09:59.245][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.248][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-03 21:09:59.250][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-03 21:09:59.251][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.254][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:09:59.255][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-03 21:09:59.258][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-03 21:09:59.259][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.262][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-03 21:09:59.264][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-03 21:09:59.265][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-03 21:09:59.266][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.269][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-03 21:09:59.271][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.287][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-03 21:09:59.288][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.289][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:59.291][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:59.293][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:59.295][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:09:59.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:59.297][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.298][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-03 21:09:59.299][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:59.300][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.301][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.302][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:59.302][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:09:59.302][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:09:59.302][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:09:59.302][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:09:59.303][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:59.304][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.306][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:59.307][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.309][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:59.310][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.311][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:59.312][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:59.313][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.314][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.315][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-03 21:09:59.317][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.318][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:09:59.319][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.320][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:59.320][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.321][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:59.322][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.323][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:59.324][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:09:59.325][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:59.326][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.327][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-03 21:09:59.328][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:59.329][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.330][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.331][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:59.331][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:09:59.331][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:09:59.331][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:09:59.331][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:09:59.332][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:59.333][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.335][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:59.336][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.337][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:59.338][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.339][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:59.340][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:59.341][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.342][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.343][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-03 21:09:59.345][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.346][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-03 21:09:59.347][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.348][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:59.349][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:59.351][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.352][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:59.353][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:09:59.353][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:59.354][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.355][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-03 21:09:59.356][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:59.357][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.358][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.359][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.360][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:59.361][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.362][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.363][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:59.364][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.366][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:59.367][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.367][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:59.368][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:59.369][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.370][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.371][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-03 21:09:59.373][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.374][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:09:59.375][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.376][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:59.377][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:09:59.379][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:59.381][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:09:59.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:59.383][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.384][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-03 21:09:59.385][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:59.390][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.391][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.392][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.393][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:09:59.394][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.396][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:59.397][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.399][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:59.400][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.400][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:59.401][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:59.402][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.403][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.404][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:59.405][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.407][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.410][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[2024-05-03 21:09:59.411][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.416][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.420][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.424][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.429][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.433][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.437][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.441][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.446][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.450][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.454][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.459][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.463][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.467][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.472][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.476][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.481][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-03 21:09:59.482][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-03 21:09:59.483][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-03 21:09:59.485][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-03 21:09:59.491][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-03 21:09:59.492][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:09:59.494][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-03 21:09:59.495][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-03 21:09:59.496][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-03 21:09:59.498][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:09:59.499][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:09:59.500][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-03 21:09:59.502][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-03 21:09:59.503][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-03 21:09:59.504][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-03 21:09:59.506][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:09:59.507][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-03 21:09:59.508][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-03 21:09:59.510][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-03 21:09:59.511][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-03 21:09:59.512][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-03 21:09:59.514][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-03 21:09:59.515][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-03 21:09:59.516][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-03 21:09:59.518][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-03 21:09:59.519][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-03 21:09:59.520][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-03 21:09:59.522][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-03 21:09:59.523][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-03 21:09:59.524][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-03 21:09:59.526][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-03 21:09:59.527][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-03 21:09:59.528][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-03 21:09:59.530][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-03 21:09:59.531][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-03 21:09:59.532][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-03 21:09:59.534][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-03 21:09:59.535][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-03 21:09:59.536][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-03 21:09:59.538][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-03 21:09:59.539][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-03 21:09:59.540][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-03 21:09:59.542][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-03 21:09:59.543][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-03 21:09:59.545][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-03 21:09:59.546][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-03 21:09:59.547][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-03 21:09:59.549][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-03 21:09:59.550][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-03 21:09:59.551][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-03 21:09:59.553][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-03 21:09:59.554][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-03 21:09:59.555][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-03 21:09:59.557][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-03 21:09:59.558][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-03 21:09:59.559][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-03 21:09:59.561][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-03 21:09:59.562][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-03 21:09:59.563][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-03 21:09:59.565][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-03 21:09:59.566][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-03 21:09:59.568][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-03 21:09:59.569][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-03 21:09:59.570][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-03 21:09:59.572][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-03 21:09:59.573][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-03 21:09:59.574][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-03 21:09:59.576][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-03 21:09:59.577][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-03 21:09:59.578][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-03 21:09:59.580][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-03 21:09:59.581][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-03 21:09:59.583][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-03 21:09:59.589][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-03 21:09:59.591][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-03 21:09:59.592][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-03 21:09:59.594][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-03 21:09:59.595][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-03 21:09:59.596][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-03 21:09:59.598][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-03 21:09:59.599][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-03 21:09:59.601][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-03 21:09:59.602][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-03 21:09:59.603][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-03 21:09:59.605][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:09:59.606][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:09:59.607][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.609][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.610][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.617][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.624][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.630][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.636][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.642][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.648][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.654][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.660][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.666][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.672][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.679][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.685][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.695][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[2024-05-03 21:09:59.696][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.702][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.707][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[2024-05-03 21:09:59.708][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.714][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:09:59.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:09:59.721][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/definitions.yml". biodb.DEBUG[2024-05-03 21:09:59.722][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:59.724][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.725][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-03 21:09:59.726][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.727][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:09:59.728][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.729][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2024-05-03 21:09:59.730][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:09:59.732][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-03 21:09:59.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:09:59.734][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.735][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2024-05-03 21:09:59.736][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2024-05-03 21:09:59.737][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2024-05-03 21:09:59.738][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-03 21:09:59.739][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:09:59.739][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2024-05-03 21:09:59.739][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2024-05-03 21:09:59.740][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-03 21:09:59.741][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.743][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:09:59.744][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:09:59.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:09:59.745][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:09:59.746][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-03 21:09:59.746][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2024-05-03 21:09:59.747][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:59.748][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:59.749][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-03 21:09:59.750][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:09:59.751][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2024-05-03 21:09:59.753][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:09:59.754][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:09:59.756][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:09:59.757][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:09:59.761][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:59.762][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2024-05-03 21:09:59.763][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:59.764][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:59.765][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:59.766][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:59.768][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2024-05-03 21:09:59.769][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.DEBUG[2024-05-03 21:09:59.770][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-03 21:09:59.770][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip". biodb.DEBUG[2024-05-03 21:09:59.771][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:09:59.771][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:09:59.772][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler. biodb.DEBUG[2024-05-03 21:09:59.773][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize". biodb.DEBUG[2024-05-03 21:09:59.774][self$registerConnector] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-03 21:09:59.776][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:59.777][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:59.778][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:59.779][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-03 21:09:59.780][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-03 21:09:59.781][self$setFrequency] t=1.000000, n=3.000000 biodb.INFO [2024-05-03 21:09:59.783][biodb::testThat] biodb.INFO [2024-05-03 21:09:59.784][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. "). biodb.INFO [2024-05-03 21:09:59.785][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:09:59.785][biodb::testThat] biodb.DEBUG[2024-05-03 21:09:59.788][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2024-05-03 21:09:59.793][private$doSearchForEntries] fields VALUES = and biodb.DEBUG[2024-05-03 21:09:59.795][private$doSearchForEntries] fields VALUES = and biodb.DEBUG[2024-05-03 21:09:59.798][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:59.799][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:59.800][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:09:59.802][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:59.803][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:09:59.804][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:09:59.805][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:09:59.806][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:09:59.807][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:09:59.808][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:09:59.809][private$doSearchForEntries] Total number of IDs = 2 biodb.DEBUG[2024-05-03 21:09:59.810][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2024-05-03 21:09:59.811][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-03 21:09:59.813][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:09:59.814][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2024-05-03 21:09:59.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001". biodb.TRACE[2024-05-03 21:09:59.817][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:09:59.819][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml". biodb.DEBUG[2024-05-03 21:09:59.820][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:09:59.822][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:09:59.823][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:09:59.824][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:09:59.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:09:59.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:09:59.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:09:59.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:09:59.832][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:09:59.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:09:59.838][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.839][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.840][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.840][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.846][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.847][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.848][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.849][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:09:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.854][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:59.855][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:59.856][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.857][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.858][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:09:59.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:09:59.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.862][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:59.863][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:59.864][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.865][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:09:59.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:09:59.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.870][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:59.872][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:59.872][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.873][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:09:59.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:09:59.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.879][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:59.880][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:59.881][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.882][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:09:59.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:09:59.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.887][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:59.888][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:59.889][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.890][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:59.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:09:59.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.895][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.896][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.902][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.903][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:09:59.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.908][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:59.909][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:59.910][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.911][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.913][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:59.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:09:59.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.917][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:59.918][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:59.919][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.919][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:59.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:09:59.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.925][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:59.926][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:59.927][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.928][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:09:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:09:59.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.933][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:59.934][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:59.935][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.936][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:09:59.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:09:59.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.941][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:59.942][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.943][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.944][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:09:59.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:09:59.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.950][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:59.951][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:59.952][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.953][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:59.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:09:59.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.958][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.959][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.960][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.961][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:09:59.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:09:59.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.966][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:59.967][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:59.968][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.969][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.971][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:09:59.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:09:59.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.975][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:59.976][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:59.977][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.978][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.979][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:09:59.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:09:59.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.983][ef$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:59.984][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:59.985][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.986][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.987][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:09:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:09:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:09:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:09:59.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:09:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:09:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.008][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.012][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.016][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.019][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.023][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.027][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.081][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.092][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.147][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.151][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.181][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.185][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.197][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.201][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.221][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:10:00.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.237][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:10:00.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.265][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.273][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:00.300][self$createEntryFromContent] Accession numbers: HMDB0000001. biodb.TRACE[2024-05-03 21:10:00.301][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.305][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.309][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:00.316][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:10:00.317][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:10:00.323][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:00.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:00.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:00.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:00.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:00.331][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:00.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:00.333][private$loadEntries] Creating entries from ids [1]: "HMDB0000002". biodb.DEBUG[2024-05-03 21:10:00.334][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-03 21:10:00.336][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.337][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.TRACE[2024-05-03 21:10:00.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002". biodb.TRACE[2024-05-03 21:10:00.341][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:10:00.342][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml". biodb.DEBUG[2024-05-03 21:10:00.343][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:10:00.344][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-03 21:10:00.345][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-03 21:10:00.347][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:00.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:00.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:00.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:00.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:00.355][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:00.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:10:00.359][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.360][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.361][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.362][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.367][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.368][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.369][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.370][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.375][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.376][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.377][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.378][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.379][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.383][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.384][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.385][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.386][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.387][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.391][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.392][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.393][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.394][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.399][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.400][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.401][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.402][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.407][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.408][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.409][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.410][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.412][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.415][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.416][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.417][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.418][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.420][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.424][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.425][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.426][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.427][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.437][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.439][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.440][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.440][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.446][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.447][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.448][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.448][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.454][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.455][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.455][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.456][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.462][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.463][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.464][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.465][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.470][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.471][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.472][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.473][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.478][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.479][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.480][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.481][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.486][ef$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.487][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.488][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.489][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.490][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.494][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.495][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.496][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.497][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.502][ef$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:10:00.503][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.504][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.505][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.507][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2024-05-03 21:10:00.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.522][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.526][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.530][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:00.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:00.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.534][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.543][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.547][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-03 21:10:00.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-03 21:10:00.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:00.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-03 21:10:00.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.586][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.590][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-03 21:10:00.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-03 21:10:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.609][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.613][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.617][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.621][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.629][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:00.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:00.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-03 21:10:00.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-03 21:10:00.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.661][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.665][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.669][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:00.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:00.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.705][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:00.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.709][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.713][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.717][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-03 21:10:00.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.721][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.724][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-03 21:10:00.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-03 21:10:00.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.732][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:10:00.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-03 21:10:00.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.763][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-03 21:10:00.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-03 21:10:00.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:00.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.793][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.797][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.806][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:00.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:00.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:00.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:00.835][self$createEntryFromContent] Accession numbers: HMDB0000002. biodb.TRACE[2024-05-03 21:10:00.836][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.840][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.844][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.848][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:00.852][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:10:00.853][private$doSearchForEntries] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:10:00.855][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:00.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:00.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:00.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:00.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:00.864][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:00.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:00.870][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2024-05-03 21:10:00.871][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular") biodb.DEBUG[2024-05-03 21:10:00.872][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular") biodb.DEBUG[2024-05-03 21:10:00.884][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.885][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.887][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:10:00.888][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.890][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:10:00.891][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:10:00.892][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:10:00.893][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:10:00.894][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:10:00.895][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:10:00.896][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2024-05-03 21:10:00.897][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.909][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.913][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.917][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.921][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:00.924][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:10:00.925][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:10:00.926][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:00.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:00.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:00.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:00.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:00.934][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:00.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:10:00.936][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.940][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.944][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.948][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.956][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:00.960][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:00.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:00.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:00.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:00.963][private$doSearchForEntries] MATCHED = FALSE biodb.DEBUG[2024-05-03 21:10:00.964][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:10:00.965][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:00.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:00.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:00.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:00.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:00.973][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:00.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:00.979][private$doSearchForEntries] fields NAMES = description biodb.DEBUG[2024-05-03 21:10:00.980][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes") biodb.DEBUG[2024-05-03 21:10:00.981][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes") biodb.DEBUG[2024-05-03 21:10:00.982][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.984][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.990][private$doGetEntryIds] .doGetEntryIds 10 biodb.DEBUG[2024-05-03 21:10:00.991][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-03 21:10:00.992][private$doGetEntryIds] .doGetEntryIds 11 biodb.DEBUG[2024-05-03 21:10:00.994][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$. biodb.DEBUG[2024-05-03 21:10:00.995][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$ biodb.DEBUG[2024-05-03 21:10:00.996][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml biodb.DEBUG[2024-05-03 21:10:00.997][private$doGetEntryIds] COUNT IDS = 2 biodb.DEBUG[2024-05-03 21:10:00.998][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002" biodb.DEBUG[2024-05-03 21:10:00.999][private$doSearchForEntries] Total number of IDs = 2 biodb.TRACE[2024-05-03 21:10:01.001][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.005][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.008][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.012][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.016][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.020][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.024][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:01.028][private$doSearchForEntries] MATCHED = FALSE biodb.DEBUG[2024-05-03 21:10:01.029][private$doSearchForEntries] COUNT IDS = 0 biodb.DEBUG[2024-05-03 21:10:01.030][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:01.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:01.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:01.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:01.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:01.038][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:01.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:10:01.040][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.044][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.048][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.052][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:01.063][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-03 21:10:01.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-03 21:10:01.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:01.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:01.067][private$doSearchForEntries] MATCHED = TRUE biodb.DEBUG[2024-05-03 21:10:01.068][private$doSearchForEntries] COUNT IDS = 1 biodb.DEBUG[2024-05-03 21:10:01.069][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:01.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:01.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:01.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:01.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:01.077][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:01.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-03 21:10:01.084][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-03 21:10:01.086][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2024-05-03 21:10:01.087][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2024-05-03 21:10:01.088][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-03 21:10:01.088][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:01.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:01.095][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:01.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:01.097][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:01.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ] > > proc.time() user system elapsed 8.707 0.518 12.497