Pierrick Roger
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: RELEASE_3_15 |
| git_last_commit: 633a5f0 |
| git_last_commit_date: 2022-09-23 13:17:22 -0400 (Fri, 23 Sep 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:01 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the biodbHmdb package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 179/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.2.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodbHmdb |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biodbHmdb_1.2.0.tar.gz |
| StartedAt: 2022-10-18 18:46:20 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 18:47:14 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 54.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biodbHmdb_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/biodbHmdb.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbHmdb/DESCRIPTION’ ... OK * this is package ‘biodbHmdb’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbHmdb’ can be installed ... OK * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.15-bioc/meat/biodbHmdb.Rcheck/00check.log’ for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Tag.cpp -o Tag.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-tag.cpp -o test-100-tag.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so RcppExports.o Tag.o extractXmlEntries.o test-100-tag.o test-runner.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
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> # 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 [2022-10-18 18:47:02.879][biodb::testContext]
biodb.INFO [2022-10-18 18:47:02.883][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:02.884][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2022-10-18 18:47:02.885][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:02.886][biodb::testContext]
biodb.INFO [2022-10-18 18:47:02.888][biodb::testThat]
biodb.INFO [2022-10-18 18:47:02.890][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2022-10-18 18:47:02.891][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:02.892][biodb::testThat]
biodb.INFO [2022-10-18 18:47:02.995][biodb::testContext]
biodb.INFO [2022-10-18 18:47:02.996][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:02.997][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-10-18 18:47:02.998][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:02.999][biodb::testContext]
biodb.INFO [2022-10-18 18:47:03.018][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:03.020][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:03.029][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:03.030][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:47:03.031][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:47:03.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.035][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:47:03.054][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:47:03.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.058][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:47:03.060][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:47:03.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.076][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:47:03.077][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:47:03.078][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:47:03.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.082][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:47:03.083][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:47:03.084][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:47:03.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.088][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:47:03.089][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:47:03.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.092][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:47:03.093][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:47:03.094][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:47:03.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.098][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:47:03.099][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:47:03.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.102][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:47:03.103][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:47:03.104][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:47:03.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.108][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:03.109][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:47:03.110][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:47:03.111][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:47:03.112][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:47:03.113][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:47:03.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.116][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:47:03.117][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:47:03.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.121][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:47:03.122][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:47:03.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.125][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:47:03.126][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:47:03.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.130][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:47:03.131][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:47:03.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.134][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:47:03.135][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:47:03.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.139][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:03.140][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:47:03.143][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:47:03.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.147][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:47:03.148][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:47:03.149][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:47:03.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.155][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:47:03.186][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.200][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:47:03.202][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.203][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:03.204][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.205][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.206][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.207][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.208][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:03.209][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:03.210][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.211][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:47:03.212][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:03.213][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.213][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.214][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:03.214][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:03.214][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:03.214][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:03.214][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:03.216][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:03.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.218][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:03.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.220][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.221][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.222][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.228][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:03.229][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:03.230][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.231][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.232][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:47:03.233][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.234][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:03.235][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.236][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:03.237][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.238][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.239][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.240][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.241][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:03.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:03.243][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.244][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:47:03.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:03.246][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.246][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.247][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:03.247][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:03.247][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:03.247][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:03.247][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:03.248][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:03.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:03.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.255][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:03.256][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:03.257][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.258][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.259][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:47:03.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.262][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:47:03.263][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.264][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:03.265][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.266][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.267][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.268][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.269][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:03.270][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:03.271][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.272][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:47:03.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:03.274][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.275][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.276][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.277][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:03.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:03.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.282][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.283][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.284][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:03.285][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:03.286][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.287][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.288][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:47:03.290][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.291][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:03.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.292][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:03.293][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.294][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.295][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.297][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:03.298][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:03.299][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.300][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:47:03.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:03.302][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.304][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.305][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:03.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.308][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:03.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.310][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.311][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.312][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:03.313][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:03.314][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.315][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.319][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:03.320][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.334][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[2022-10-18 18:47:03.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.364][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[2022-10-18 18:47:03.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.400][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:47:03.404][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:47:03.406][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:47:03.407][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:47:03.409][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:47:03.410][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:03.411][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:03.412][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:03.414][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:47:03.415][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:03.416][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:03.418][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:47:03.419][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:03.420][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:03.422][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:47:03.423][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:03.424][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:47:03.425][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:47:03.427][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:47:03.428][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:47:03.429][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:47:03.431][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:47:03.432][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:47:03.433][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:47:03.435][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:47:03.436][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:47:03.437][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:47:03.439][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:47:03.440][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:47:03.441][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:47:03.443][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:47:03.444][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:47:03.445][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:47:03.446][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:47:03.448][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:47:03.449][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:47:03.450][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:47:03.452][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:47:03.453][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:47:03.454][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:47:03.456][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:47:03.457][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:47:03.458][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:47:03.460][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:47:03.461][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:47:03.462][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:47:03.463][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:47:03.465][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:47:03.466][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:47:03.467][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:47:03.469][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:47:03.470][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:47:03.471][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:47:03.473][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:47:03.474][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:47:03.475][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:47:03.477][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:47:03.478][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:47:03.479][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:47:03.481][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:47:03.482][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:47:03.483][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:47:03.485][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:47:03.486][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:47:03.487][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:47:03.489][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:47:03.490][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:47:03.491][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:47:03.493][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:47:03.494][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:47:03.495][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:47:03.497][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:47:03.498][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:47:03.499][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:47:03.501][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:47:03.502][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:47:03.503][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:47:03.505][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:47:03.506][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:47:03.507][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:47:03.509][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:47:03.510][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:47:03.511][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:47:03.517][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:47:03.518][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:03.521][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:03.522][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.563][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:03.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:03.684][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:03.693][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:03.695][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.697][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.699][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:03.700][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.701][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2022-10-18 18:47:03.702][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.704][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:47:03.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:03.706][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.707][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2022-10-18 18:47:03.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2022-10-18 18:47:03.709][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2022-10-18 18:47:03.710][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:03.711][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:03.711][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2022-10-18 18:47:03.712][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:47:03.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:03.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:03.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:03.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:03.724][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-10-18 18:47:03.724][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2022-10-18 18:47:03.725][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:03.726][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:03.727][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:03.729][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:03.735][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:03.737][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:03.739][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:03.740][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:03.769][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:03.770][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2022-10-18 18:47:03.775][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:03.779][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:03.784][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:03.785][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:03.786][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2022-10-18 18:47:03.788][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2022-10-18 18:47:03.789][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-10-18 18:47:03.789][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2022-10-18 18:47:03.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:03.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:03.792][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2022-10-18 18:47:03.792][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2022-10-18 18:47:03.794][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:03.811][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:03.812][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:03.813][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:03.815][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:03.816][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:03.817][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2022-10-18 18:47:03.834][biodb::testThat]
biodb.INFO [2022-10-18 18:47:03.835][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2022-10-18 18:47:03.836][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:03.837][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:03.841][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2022-10-18 18:47:03.846][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:03.850][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:03.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:03.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.869][FUN] Functions in observer BiodbConfig: [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[2022-10-18 18:47:03.882][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.883][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.884][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.885][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.916][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:03.917][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:03.918][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.919][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.943][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:03.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:03.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.950][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:03.951][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:03.952][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.953][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.955][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:03.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:03.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.962][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.963][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.964][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.965][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.973][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:03.974][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:03.975][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.976][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:03.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:03.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.985][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.986][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.987][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.988][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.989][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.997][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:03.998][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:03.999][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.000][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.008][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.009][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.010][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.011][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.020][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.021][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.022][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.022][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.031][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.038][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.038][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.046][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.047][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.048][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.049][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.057][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.058][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.059][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.060][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.068][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.069][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.070][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.071][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.081][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.083][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.084][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.093][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.094][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.096][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.097][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.105][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.106][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.107][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.107][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.116][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:04.117][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.118][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.118][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.171][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.175][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.179][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.183][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:04.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:04.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.187][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:04.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.191][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:04.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:04.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.242][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.254][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.262][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.267][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.320][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.324][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.328][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.363][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.379][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:04.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.400][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:04.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:04.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.457][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.465][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:04.496][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2022-10-18 18:47:04.501][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:04.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:04.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:04.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.513][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:04.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.541][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.581][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.585][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.589][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:04.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.613][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.614][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.615][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.616][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.640][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.641][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.642][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.643][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:04.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.658][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.662][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.666][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.667][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.668][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.669][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:04.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.698][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.699][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.700][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.701][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:04.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.712][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.716][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.720][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.724][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.725][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.726][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.727][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.728][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:04.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.749][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.750][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.751][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.752][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.764][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.772][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.775][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.776][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.777][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.778][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:04.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:04.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.795][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.806][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.807][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.808][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.809][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:04.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.820][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.824][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.828][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.832][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.833][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.834][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.835][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.836][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.859][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.860][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.860][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.861][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:04.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.885][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.886][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.887][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.888][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:04.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.909][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.918][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.919][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.920][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.921][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.922][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:04.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.937][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.949][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.950][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.951][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.952][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:04.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.972][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.976][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.977][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.978][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.979][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:04.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:04.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:04.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:04.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:04.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.007][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.008][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.032][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.033][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.034][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.035][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.051][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.055][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.059][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.063][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.064][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.065][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.066][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.079][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.080][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.081][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.082][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.088][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.089][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.090][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.091][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.096][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.098][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.099][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.100][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.108][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.109][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.114][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.116][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.117][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.118][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.124][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.125][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.126][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.127][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.133][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.134][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.135][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.136][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.141][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.142][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.143][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.144][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.150][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.151][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.152][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.153][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.158][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:05.159][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:05.160][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.161][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.173][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.174][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.175][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.176][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.182][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.183][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.184][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.189][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.190][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.191][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.192][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.200][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.201][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.206][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.208][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.209][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.210][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.215][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.216][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.217][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.218][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.224][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:05.225][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:05.226][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.227][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:05.233][biodb::testThat]
biodb.INFO [2022-10-18 18:47:05.234][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-18 18:47:05.235][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:05.236][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:05.249][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2022-10-18 18:47:05.257][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-10-18 18:47:05.261][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:05.263][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-10-18 18:47:05.265][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2022-10-18 18:47:05.266][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:05.269][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2022-10-18 18:47:05.270][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:05.319][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:05.320][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:05.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:05.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:05.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:05.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:05.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:05.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:05.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:05.337][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.338][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.339][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.340][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.348][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.349][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.350][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.351][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.353][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.360][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.361][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.362][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.363][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.372][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.374][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.374][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.383][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.384][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.385][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.385][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.394][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.395][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.395][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.396][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.405][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.406][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.407][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.408][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.409][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.421][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.422][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.423][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.424][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.432][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.433][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.434][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.435][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.444][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:05.445][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:05.446][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.447][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:05.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:05.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.455][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.456][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.457][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.458][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.466][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.468][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.468][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.469][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.478][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.479][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.480][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.481][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.490][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.491][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.492][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.493][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.501][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.502][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.503][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.504][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.505][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.512][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:05.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:05.515][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.516][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:05.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:05.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.524][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:05.525][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.526][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.527][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:05.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.555][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.559][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:05.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.563][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:05.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:05.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.597][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.609][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.613][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:05.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:05.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.640][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:05.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:05.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:05.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:05.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:05.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:05.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:05.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.687][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.691][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:05.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:05.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:05.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:05.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:05.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:05.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:05.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.741][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:05.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.756][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:05.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:05.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.790][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:05.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:05.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.794][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:05.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:05.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.802][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:05.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:05.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:05.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:05.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:05.832][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2022-10-18 18:47:05.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-18 18:47:05.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-18 18:47:05.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-18 18:47:05.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-18 18:47:05.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-18 18:47:05.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-18 18:47:05.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:05.850][biodb::testThat]
biodb.INFO [2022-10-18 18:47:05.851][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-18 18:47:05.852][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:05.853][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:05.856][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.857][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.858][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.859][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:05.860][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2022-10-18 18:47:05.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:05.908][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2022-10-18 18:47:05.917][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2022-10-18 18:47:05.918][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-10-18 18:47:05.919][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-10-18 18:47:05.921][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:05.922][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:05.923][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:05.925][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:05.926][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:05.930][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:05.931][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:05.932][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:05.933][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:05.934][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-10-18 18:47:05.935][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-10-18 18:47:05.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:05.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:05.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:05.952][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:05.953][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-10-18 18:47:05.954][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2022-10-18 18:47:05.967][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.968][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.969][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.970][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:05.971][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2022-10-18 18:47:05.984][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.988][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:05.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:05.997][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:05.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:05.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:06.002][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[2022-10-18 18:47:06.060][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-10-18 18:47:06.061][private$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[2022-10-18 18:47:06.062][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2022-10-18 18:47:06.075][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:06.077][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:06.078][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:06.080][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:06.081][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:06.102][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:06.104][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:06.105][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:06.105][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:06.106][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-10-18 18:47:06.107][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-10-18 18:47:06.109][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:06.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:06.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.113][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:06.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:06.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.117][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:06.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:06.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.120][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:06.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:06.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:06.124][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:06.125][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-10-18 18:47:06.126][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2022-10-18 18:47:06.139][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.141][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2022-10-18 18:47:06.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:06.142][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:06.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:06.189][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2022-10-18 18:47:06.190][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-10-18 18:47:06.191][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-10-18 18:47:06.213][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:06.215][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:06.217][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:06.218][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:06.219][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:06.223][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:06.224][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:06.225][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:06.226][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:06.227][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-10-18 18:47:06.228][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-10-18 18:47:06.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:06.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:06.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:06.245][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:06.246][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2022-10-18 18:47:06.260][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.261][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2022-10-18 18:47:06.262][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:06.263][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:06.288][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.293][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:06.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:06.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.300][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:06.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:06.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:06.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.356][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:06.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:06.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:06.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:06.366][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.367][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-18 18:47:06.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:06.369][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.374][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.375][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-18 18:47:06.376][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:06.376][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.381][biodb::testThat]
biodb.INFO [2022-10-18 18:47:06.382][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-18 18:47:06.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:06.384][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:06.387][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2022-10-18 18:47:07.434][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2022-10-18 18:47:07.504][biodb::testThat]
biodb.INFO [2022-10-18 18:47:07.506][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-18 18:47:07.508][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:07.509][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:07.739][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2022-10-18 18:47:07.793][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:07.795][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:07.796][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.797][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.798][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:07.800][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:07.801][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.802][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:07.804][biodb::testThat]
biodb.INFO [2022-10-18 18:47:07.805][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2022-10-18 18:47:07.806][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:07.807][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:07.810][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-10-18 18:47:07.870][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-10-18 18:47:07.872][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:07.874][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-10-18 18:47:07.891][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-10-18 18:47:07.893][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:07.894][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:07.895][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:07.897][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:07.913][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:07.915][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:07.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:07.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:07.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:07.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:07.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:07.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:07.927][FUN] Functions in observer BiodbConfig: [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[2022-10-18 18:47:07.929][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:07.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.933][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:07.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:07.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:07.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:07.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:07.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:07.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:07.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:07.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:07.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:07.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:07.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:07.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:07.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:07.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:07.974][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-10-18 18:47:07.976][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-10-18 18:47:07.992][biodb::testThat]
biodb.INFO [2022-10-18 18:47:07.994][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-10-18 18:47:07.995][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:07.996][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:08.002][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2022-10-18 18:47:08.004][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2022-10-18 18:47:08.005][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-10-18 18:47:08.006][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.008][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-10-18 18:47:08.010][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2022-10-18 18:47:08.011][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:08.013][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:08.014][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:08.015][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.032][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:08.034][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:08.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:08.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:08.049][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:08.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:08.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.053][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:08.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:08.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:08.089][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-10-18 18:47:08.090][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-10-18 18:47:08.091][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2022-10-18 18:47:08.117][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.119][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2022-10-18 18:47:08.120][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.121][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.147][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.149][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2022-10-18 18:47:08.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.151][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:08.155][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.157][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.159][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:08.160][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.162][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:08.169][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:08.170][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:08.172][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:08.173][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2022-10-18 18:47:08.218][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.220][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2022-10-18 18:47:08.221][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.222][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:08.225][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.227][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.228][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:08.230][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.231][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:08.237][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:08.238][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:08.239][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:08.240][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2022-10-18 18:47:08.253][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:08.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:08.255][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.256][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.257][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:08.258][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:08.258][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.259][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:08.260][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:47:08.261][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2022-10-18 18:47:08.269][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2022-10-18 18:47:08.270][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:47:08.270][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.272][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.274][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.275][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.INFO [2022-10-18 18:47:08.279][biodb::testContext]
biodb.INFO [2022-10-18 18:47:08.280][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:08.280][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2022-10-18 18:47:08.281][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:08.282][biodb::testContext]
biodb.INFO [2022-10-18 18:47:08.289][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:08.290][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:08.294][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:08.295][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:47:08.296][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:47:08.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.299][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:47:08.300][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:47:08.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.304][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:47:08.305][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:47:08.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.309][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:47:08.310][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:47:08.317][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:47:08.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.321][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:47:08.322][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:47:08.323][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:47:08.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.326][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:47:08.327][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:47:08.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.331][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:47:08.331][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:47:08.332][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:47:08.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.336][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:47:08.337][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:47:08.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.340][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[2022-10-18 18:47:08.341][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:47:08.342][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:47:08.343][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:47:08.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.346][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:08.347][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:47:08.348][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:47:08.349][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:47:08.350][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:47:08.351][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:47:08.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.355][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:47:08.356][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:47:08.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.360][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:47:08.361][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:47:08.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.364][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[2022-10-18 18:47:08.364][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:47:08.366][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:47:08.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.369][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:47:08.370][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:47:08.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.374][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:47:08.375][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:47:08.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.379][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:08.380][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:47:08.384][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:47:08.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.388][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:47:08.389][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:47:08.390][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:47:08.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.395][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:47:08.397][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.399][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:47:08.400][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.401][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:08.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.406][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:08.415][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:08.416][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.417][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:47:08.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:08.419][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.420][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.421][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:08.421][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:08.421][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:08.421][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:08.421][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:08.422][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:08.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.425][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:08.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.428][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.429][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:08.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:08.432][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.434][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.435][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:47:08.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:08.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.441][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:08.442][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.443][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.444][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.445][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.446][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:08.447][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:08.448][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.449][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:47:08.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:08.451][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.453][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:08.453][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:08.453][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:08.453][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:08.453][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:08.454][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:08.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.456][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:08.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.459][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.460][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:08.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:08.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.464][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.465][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:47:08.467][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.468][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:47:08.469][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:08.471][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.473][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.476][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:08.477][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:08.478][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.479][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:47:08.480][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:08.480][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.482][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.483][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:08.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.486][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:08.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.489][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.490][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:08.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:08.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.494][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.495][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:47:08.497][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.497][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:08.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:08.500][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.507][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.509][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.510][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:08.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:08.512][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.513][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:47:08.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:08.515][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.517][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.518][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:08.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:08.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.523][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.524][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:08.526][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:08.527][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.528][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.529][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:08.530][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.611][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:47:08.613][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:47:08.614][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:47:08.615][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:47:08.617][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:47:08.618][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:08.619][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:08.621][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:08.622][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:47:08.623][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:08.624][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:08.626][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:47:08.627][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:08.628][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:08.630][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:47:08.631][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:08.632][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:47:08.633][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:47:08.635][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:47:08.636][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:47:08.637][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:47:08.638][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:47:08.640][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:47:08.641][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:47:08.642][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:47:08.644][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:47:08.645][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:47:08.646][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:47:08.647][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:47:08.649][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:47:08.650][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:47:08.651][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:47:08.652][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:47:08.654][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:47:08.655][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:47:08.656][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:47:08.657][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:47:08.659][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:47:08.660][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:47:08.661][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:47:08.663][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:47:08.664][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:47:08.665][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:47:08.667][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:47:08.668][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:47:08.669][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:47:08.676][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:47:08.678][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:47:08.680][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:47:08.681][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:47:08.682][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:47:08.684][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:47:08.685][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:47:08.686][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:47:08.688][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:47:08.689][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:47:08.690][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:47:08.692][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:47:08.693][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:47:08.695][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:47:08.696][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:47:08.697][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:47:08.699][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:47:08.700][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:47:08.702][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:47:08.703][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:47:08.704][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:47:08.706][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:47:08.707][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:47:08.708][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:47:08.710][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:47:08.711][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:47:08.713][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:47:08.714][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:47:08.715][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:47:08.717][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:47:08.718][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:47:08.720][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:47:08.721][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:47:08.723][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:47:08.724][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:47:08.726][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:47:08.727][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:47:08.729][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:47:08.731][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:08.732][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:08.733][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.735][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.817][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[2022-10-18 18:47:08.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:08.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:08.853][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:08.855][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:08.857][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.857][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.858][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.859][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:08.860][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.861][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2022-10-18 18:47:08.862][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.863][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.864][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:47:08.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:08.866][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.867][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2022-10-18 18:47:08.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2022-10-18 18:47:08.869][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2022-10-18 18:47:08.870][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:08.871][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:08.871][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2022-10-18 18:47:08.872][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:47:08.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:08.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:08.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:08.877][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:08.878][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-10-18 18:47:08.878][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2022-10-18 18:47:08.879][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:08.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:08.881][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:08.882][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:08.883][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:08.884][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:08.886][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:08.887][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:08.890][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:08.891][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2022-10-18 18:47:08.892][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:08.894][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:08.895][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:08.896][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:08.897][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2022-10-18 18:47:08.898][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2022-10-18 18:47:08.899][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-10-18 18:47:08.899][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2022-10-18 18:47:08.900][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:08.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:08.901][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2022-10-18 18:47:08.902][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2022-10-18 18:47:08.903][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:08.905][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:08.906][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:08.907][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:08.908][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:08.909][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:08.910][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2022-10-18 18:47:08.911][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.912][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2022-10-18 18:47:08.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.914][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:08.918][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.919][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.921][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:08.922][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.923][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:08.927][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:08.928][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:08.929][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:08.930][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:08.932][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2022-10-18 18:47:08.940][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.942][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2022-10-18 18:47:08.943][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.944][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:08.946][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2022-10-18 18:47:08.947][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-10-18 18:47:08.948][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:08.950][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-10-18 18:47:08.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2022-10-18 18:47:08.953][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:08.955][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2022-10-18 18:47:08.956][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:08.970][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:08.972][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:08.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:08.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:08.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:08.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:08.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:08.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:08.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:08.986][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.988][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.989][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:08.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:08.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.997][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:08.998][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:08.999][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.000][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.002][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.009][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.010][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.011][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.012][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.013][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.020][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.021][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.022][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.023][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.037][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.038][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.039][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.040][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.049][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.051][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.052][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.053][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.061][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.062][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.064][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.065][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.073][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.074][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.076][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.084][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.085][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.086][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.087][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.088][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.095][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:09.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:09.097][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.098][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:09.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:09.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.107][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:09.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:09.109][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.110][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:09.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:09.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.120][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.121][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.128][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.139][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.140][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.140][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.149][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.150][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.151][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.152][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.160][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:09.161][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:09.162][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.163][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.164][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:09.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:09.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:09.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:09.173][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.174][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:09.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:09.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.182][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:09.183][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.184][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.185][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.186][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:09.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.204][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.208][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.212][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:09.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.221][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.224][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.228][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:09.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:09.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.254][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.261][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:09.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:09.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.276][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.280][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:09.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.288][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:09.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:09.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:09.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.296][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:09.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:09.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:09.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:09.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:09.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:09.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.505][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:09.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:09.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:09.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:09.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:09.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:09.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:09.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:09.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.520][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.531][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.534][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:09.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:09.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.564][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:09.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:09.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:09.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.578][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:09.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:09.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.582][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:09.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:09.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.586][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:09.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.602][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:09.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:09.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:09.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.636][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:09.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:09.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.640][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:09.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:09.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.648][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:09.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:09.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:09.680][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2022-10-18 18:47:09.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:09.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:09.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:09.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:09.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:09.697][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:47:09.698][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2022-10-18 18:47:09.699][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2022-10-18 18:47:09.700][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:47:09.701][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:09.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:09.703][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.705][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:47:09.710][biodb::testContext]
biodb.INFO [2022-10-18 18:47:09.711][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:09.712][biodb::testContext] Test context - Test search of entries
biodb.INFO [2022-10-18 18:47:09.713][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:09.714][biodb::testContext]
biodb.INFO [2022-10-18 18:47:09.721][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:09.722][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:09.726][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:09.728][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:47:09.729][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:47:09.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.733][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:47:09.734][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:47:09.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.738][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:47:09.739][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:47:09.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.743][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:47:09.744][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:47:09.745][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:47:09.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.748][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:47:09.749][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:47:09.750][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:47:09.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.754][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:47:09.755][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:47:09.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.759][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:47:09.760][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:47:09.761][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:47:09.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.765][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:47:09.766][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:47:09.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.770][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:47:09.771][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:47:09.772][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:47:09.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.776][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:09.777][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:47:09.778][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:47:09.779][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:47:09.780][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:47:09.782][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:47:09.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.785][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:47:09.787][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:47:09.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.790][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:47:09.792][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:47:09.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.795][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:47:09.797][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:47:09.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.800][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:47:09.802][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:47:09.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.805][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:47:09.806][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:47:09.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.810][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:09.811][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:47:09.816][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:47:09.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.820][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:47:09.821][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:47:09.822][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:47:09.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.827][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:47:09.828][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.836][self$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[2022-10-18 18:47:09.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.838][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:09.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.842][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.843][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:09.844][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:09.845][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.846][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:47:09.847][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:09.848][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.849][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.850][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:09.850][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:09.850][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:09.850][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:09.850][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:09.851][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:09.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.854][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:09.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.857][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.858][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:09.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:09.860][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.861][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.862][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:47:09.864][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.865][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:09.866][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.867][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:09.868][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.869][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.870][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.872][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:09.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:09.874][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.875][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:47:09.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:09.877][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:09.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:09.879][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:09.879][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:09.879][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:09.880][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:09.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:09.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.886][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:09.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:09.889][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.890][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.891][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:47:09.893][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.894][self$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[2022-10-18 18:47:09.895][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.896][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:09.896][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.897][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.898][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.899][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.900][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:09.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:09.902][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.903][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:47:09.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:09.905][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.906][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.907][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:09.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:09.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.915][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:09.917][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:09.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.919][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.920][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:47:09.922][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.923][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:09.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.925][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:09.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.927][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.928][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.929][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:09.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:09.931][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.932][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:47:09.933][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:09.934][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.935][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:09.936][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.937][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:09.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.940][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:09.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:09.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:09.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:09.943][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.944][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:09.945][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:09.946][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:09.947][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:09.948][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:09.949][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.967][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[2022-10-18 18:47:09.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:09.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:09.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:09.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:09.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:09.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.002][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[2022-10-18 18:47:10.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.025][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:47:10.026][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:47:10.028][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:47:10.029][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:47:10.030][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:47:10.032][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:10.033][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:10.035][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:10.036][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:47:10.037][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:10.038][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:10.040][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:47:10.041][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:10.043][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:10.044][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:47:10.045][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:10.047][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:47:10.048][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:47:10.049][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:47:10.051][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:47:10.052][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:47:10.054][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:47:10.055][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:47:10.056][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:47:10.058][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:47:10.059][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:47:10.060][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:47:10.062][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:47:10.063][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:47:10.064][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:47:10.066][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:47:10.067][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:47:10.068][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:47:10.070][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:47:10.071][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:47:10.072][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:47:10.073][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:47:10.075][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:47:10.076][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:47:10.077][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:47:10.079][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:47:10.080][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:47:10.081][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:47:10.083][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:47:10.084][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:47:10.085][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:47:10.087][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:47:10.088][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:47:10.089][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:47:10.091][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:47:10.092][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:47:10.093][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:47:10.095][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:47:10.096][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:47:10.097][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:47:10.098][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:47:10.100][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:47:10.101][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:47:10.102][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:47:10.104][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:47:10.105][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:47:10.110][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:47:10.113][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:47:10.114][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:47:10.115][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:47:10.117][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:47:10.118][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:47:10.120][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:47:10.121][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:47:10.123][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:47:10.124][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:47:10.125][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:47:10.127][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:47:10.128][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:47:10.130][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:47:10.131][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:47:10.133][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:47:10.134][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:47:10.136][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:47:10.137][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:47:10.139][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:47:10.140][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:47:10.142][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:47:10.143][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:47:10.162][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:10.163][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:10.164][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.166][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.167][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[2022-10-18 18:47:10.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.207][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[2022-10-18 18:47:10.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.220][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[2022-10-18 18:47:10.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.227][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[2022-10-18 18:47:10.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.233][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[2022-10-18 18:47:10.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.246][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[2022-10-18 18:47:10.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.267][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[2022-10-18 18:47:10.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:10.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.281][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:10.283][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:10.285][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:10.286][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:47:10.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:10.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:10.289][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:10.290][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2022-10-18 18:47:10.291][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:10.292][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:10.293][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:47:10.294][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:10.295][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:10.296][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2022-10-18 18:47:10.297][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2022-10-18 18:47:10.298][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2022-10-18 18:47:10.300][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:10.301][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:10.301][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2022-10-18 18:47:10.302][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:47:10.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:10.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:10.305][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:10.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:10.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:10.308][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:10.309][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-10-18 18:47:10.309][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2022-10-18 18:47:10.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:10.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:10.312][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:10.313][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:10.314][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:10.316][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:10.317][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:10.319][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:10.322][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:10.323][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2022-10-18 18:47:10.325][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:10.326][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:10.328][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:10.329][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:10.330][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2022-10-18 18:47:10.331][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2022-10-18 18:47:10.332][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-10-18 18:47:10.332][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2022-10-18 18:47:10.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:10.334][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:10.335][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2022-10-18 18:47:10.336][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2022-10-18 18:47:10.337][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2022-10-18 18:47:10.339][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:10.340][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:10.341][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:10.343][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.15-bioc/R/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2022-10-18 18:47:10.344][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:10.345][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2022-10-18 18:47:10.346][biodb::testThat]
biodb.INFO [2022-10-18 18:47:10.347][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2022-10-18 18:47:10.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:10.349][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:10.361][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-10-18 18:47:10.362][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2022-10-18 18:47:10.363][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2022-10-18 18:47:10.366][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:10.368][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:10.369][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:10.371][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:10.372][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:10.376][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:10.377][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:10.378][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:10.379][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:10.380][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-10-18 18:47:10.381][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2022-10-18 18:47:10.383][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2022-10-18 18:47:10.384][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-10-18 18:47:10.386][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:10.387][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-10-18 18:47:10.389][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2022-10-18 18:47:10.390][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:10.392][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2022-10-18 18:47:10.393][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:10.409][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:10.410][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:10.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:10.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:10.427][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.429][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.430][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.438][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.439][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.440][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.441][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.443][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.450][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.451][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.452][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.453][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.455][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.462][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.464][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.465][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.473][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.474][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.475][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.476][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.484][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.485][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.486][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.487][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.489][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.496][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.497][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.498][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.499][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.500][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.515][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.516][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.517][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.518][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.526][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.527][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.528][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.529][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.537][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:10.538][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:10.539][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.539][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:10.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:10.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.547][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:10.548][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:10.549][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.550][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:10.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:10.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.558][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.559][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.560][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.561][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.571][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.572][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.580][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.581][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.582][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.583][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.590][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.591][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.592][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.593][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.594][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.600][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:10.601][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:10.602][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.603][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.604][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:10.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:10.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.611][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:10.612][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.612][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.613][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.615][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:10.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.633][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.636][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.640][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.644][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.648][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.652][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:10.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:10.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:10.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:10.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.698][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:10.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:10.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.714][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.717][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.721][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:10.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:10.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:10.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:10.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:10.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:10.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:10.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:10.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:10.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:10.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:10.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:10.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.748][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.760][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.768][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:10.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:10.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.795][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.799][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:10.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.806][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:10.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:10.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.810][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:10.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:10.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.814][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:10.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:10.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.818][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:10.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.839][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:10.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:10.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:10.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:10.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:10.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:10.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:10.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:10.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:10.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:10.912][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2022-10-18 18:47:10.913][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.917][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.921][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.924][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:10.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:10.928][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:10.929][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-10-18 18:47:10.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:10.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:10.941][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2022-10-18 18:47:10.942][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-10-18 18:47:10.944][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:10.945][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-10-18 18:47:10.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2022-10-18 18:47:10.949][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:10.950][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2022-10-18 18:47:10.951][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:10.966][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:10.967][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-10-18 18:47:10.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:10.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:10.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:10.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:10.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:10.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:10.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:10.982][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.983][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.984][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.985][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:10.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:10.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.994][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.995][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.996][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:10.997][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:10.998][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:10.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.005][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.006][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.007][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.008][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.019][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.020][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.028][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.029][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.030][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.031][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.039][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.041][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.042][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.043][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.044][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.051][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.052][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.053][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.054][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.055][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.062][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.063][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.064][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.065][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.072][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.073][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.074][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.075][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.083][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:11.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:11.085][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.086][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.087][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:11.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:11.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:11.094][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:11.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.096][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:11.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:11.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.106][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.107][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.115][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.116][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.116][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.117][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.125][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.127][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.128][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.136][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.137][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.138][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.138][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.140][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.146][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:11.147][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:11.153][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.154][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.155][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:11.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:11.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.162][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:11.163][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.163][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.164][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.166][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-10-18 18:47:11.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.183][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.186][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.190][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.194][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.197][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.201][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-18 18:47:11.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:11.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-10-18 18:47:11.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:11.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-10-18 18:47:11.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-10-18 18:47:11.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.260][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.264][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.268][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:11.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:11.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:11.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:11.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:11.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:11.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:11.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:11.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:11.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.305][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.309][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.312][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.347][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:11.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:11.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:11.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.358][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:11.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.362][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:11.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.377][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-10-18 18:47:11.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:11.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.407][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:11.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.411][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:11.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:11.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.418][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:11.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:11.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:11.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:11.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.449][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2022-10-18 18:47:11.451][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.455][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.465][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.468][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.472][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:11.473][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:11.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:11.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:11.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:11.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:11.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:11.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.496][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-10-18 18:47:11.497][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2022-10-18 18:47:11.498][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2022-10-18 18:47:11.499][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:11.501][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:11.502][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:11.503][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:11.504][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:11.508][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:11.509][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:11.510][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:11.511][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:11.512][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-10-18 18:47:11.513][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-10-18 18:47:11.514][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.518][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.522][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.526][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.529][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.533][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.537][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.541][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:11.541][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-10-18 18:47:11.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:11.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:11.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:11.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:11.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:11.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:11.553][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.557][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.561][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.565][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.569][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.573][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.576][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.580][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2022-10-18 18:47:11.581][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-10-18 18:47:11.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:11.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:11.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:11.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:11.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:11.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.603][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-10-18 18:47:11.604][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2022-10-18 18:47:11.605][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2022-10-18 18:47:11.607][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:11.608][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:11.609][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-10-18 18:47:11.611][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-10-18 18:47:11.612][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-10-18 18:47:11.616][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-10-18 18:47:11.617][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-10-18 18:47:11.618][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-10-18 18:47:11.619][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-10-18 18:47:11.620][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-10-18 18:47:11.621][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-10-18 18:47:11.622][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.626][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.630][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.634][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.637][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.641][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.645][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.649][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2022-10-18 18:47:11.650][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2022-10-18 18:47:11.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:11.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:11.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:11.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:11.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:11.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:11.661][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.666][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.670][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.673][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.677][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.681][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.685][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-18 18:47:11.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-18 18:47:11.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.689][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-10-18 18:47:11.690][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-10-18 18:47:11.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:11.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:11.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:11.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:11.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:11.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:47:11.703][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:47:11.704][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2022-10-18 18:47:11.705][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2022-10-18 18:47:11.706][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:47:11.707][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:11.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:11.709][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:11.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:11.710][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 186 ]
>
> proc.time()
user system elapsed
9.167 0.650 10.880
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 1.743 | 0.236 | 1.980 | |
| HmdbMetabolitesEntry | 0.282 | 0.013 | 0.295 | |