Pierrick Roger
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: RELEASE_3_14 |
| git_last_commit: b0dabfe |
| git_last_commit_date: 2021-11-24 05:04:38 -0400 (Wed, 24 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:41 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 177/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.0.3 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodbHmdb |
| Version: 1.0.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.0.3.tar.gz |
| StartedAt: 2022-04-12 10:51:39 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 10:53:16 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 96.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbHmdb.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbHmdb/DESCRIPTION’ ... OK * this is package ‘biodbHmdb’ version ‘1.0.3’ * 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 ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbHmdb.Rcheck/00check.log’ for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Tag.cpp -o Tag.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c extractXmlEntries.cpp -o extractXmlEntries.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c test-100-tag.cpp -o test-100-tag.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o biodbHmdb.so RcppExports.o Tag.o extractXmlEntries.o test-100-tag.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2022-04-12 10:52:48.258][biodb::testContext]
biodb.INFO [2022-04-12 10:52:48.272][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:48.274][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2022-04-12 10:52:48.276][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:48.278][biodb::testContext]
biodb.INFO [2022-04-12 10:52:48.281][biodb::testThat]
biodb.INFO [2022-04-12 10:52:48.283][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2022-04-12 10:52:48.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:48.287][biodb::testThat]
biodb.INFO [2022-04-12 10:52:48.488][biodb::testContext]
biodb.INFO [2022-04-12 10:52:48.490][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:48.491][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-04-12 10:52:48.493][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:48.495][biodb::testContext]
biodb.INFO [2022-04-12 10:52:48.538][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:52:48.541][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:52:48.554][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:48.555][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:52:48.557][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:52:48.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.566][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:52:48.609][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:52:48.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.618][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:52:48.620][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:52:48.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.626][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:52:48.628][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:52:48.630][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:52:48.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.637][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:52:48.639][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:52:48.641][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:52:48.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.649][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:52:48.650][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:52:48.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.658][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:52:48.660][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:52:48.662][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:52:48.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.670][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:52:48.671][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:52:48.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.676][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[2022-04-12 10:52:48.679][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:52:48.681][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:52:48.684][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:52:48.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.691][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:52:48.694][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:52:48.707][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:52:48.709][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:52:48.710][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:52:48.712][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:52:48.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.718][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:52:48.720][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:52:48.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.725][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:52:48.726][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:52:48.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.732][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:52:48.734][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:52:48.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.741][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:52:48.743][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:52:48.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.748][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:52:48.750][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:52:48.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.758][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:52:48.760][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:52:48.771][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:52:48.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.778][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:52:48.780][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:52:48.781][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:52:48.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:48.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:48.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:48.791][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:52:48.859][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:48.889][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:52:48.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:48.894][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:48.898][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:48.900][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:48.901][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:52:48.903][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:48.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.907][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:52:48.909][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:48.911][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:48.912][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.914][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:48.914][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:48.914][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:48.914][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:52:48.914][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:52:48.915][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:48.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:48.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:48.920][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:48.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:48.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:48.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:48.926][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:48.927][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:48.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:48.931][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:48.932][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:48.935][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:52:48.939][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:48.941][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:52:48.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:48.947][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:48.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:48.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:48.955][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:52:48.957][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:48.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.960][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:52:48.962][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:48.964][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:48.966][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.968][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:48.968][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:48.968][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:48.968][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:52:48.968][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:52:48.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:48.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:48.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:48.974][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:48.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:48.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:48.980][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:48.983][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:48.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:48.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:48.988][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:48.990][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:48.992][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:52:48.995][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:48.997][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:52:48.999][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:49.004][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.006][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.008][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.009][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.010][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:52:49.012][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:49.013][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.015][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:52:49.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:49.018][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.020][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.021][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.023][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:49.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:49.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:49.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:49.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:49.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:49.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.036][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.038][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:49.040][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:49.041][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.043][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.045][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:52:49.049][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.051][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:52:49.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.055][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:49.057][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.066][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:52:49.068][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:49.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.071][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:52:49.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:49.074][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.078][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.080][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:49.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:49.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:49.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:49.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:49.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:49.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.094][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:49.096][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:49.098][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.100][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.108][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:49.110][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.200][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[2022-04-12 10:52:49.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.233][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[2022-04-12 10:52:49.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.260][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:52:49.268][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:52:49.271][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:52:49.274][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:52:49.277][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:52:49.280][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:52:49.283][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:52:49.286][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:52:49.288][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:52:49.291][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:52:49.294][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:52:49.296][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:52:49.299][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:52:49.302][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:52:49.304][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:52:49.307][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:52:49.309][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:52:49.312][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:52:49.314][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:52:49.317][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:52:49.320][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:52:49.323][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:52:49.326][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:52:49.329][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:52:49.331][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:52:49.334][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:52:49.337][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:52:49.340][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:52:49.342][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:52:49.345][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:52:49.348][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:52:49.351][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:52:49.355][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:52:49.357][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:52:49.360][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:52:49.363][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:52:49.366][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:52:49.369][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:52:49.371][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:52:49.374][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:52:49.376][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:52:49.379][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:52:49.381][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:52:49.383][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:52:49.386][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:52:49.389][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:52:49.392][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:52:49.395][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:52:49.398][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:52:49.400][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:52:49.403][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:52:49.406][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:52:49.408][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:52:49.410][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:52:49.412][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:52:49.415][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:52:49.418][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:52:49.421][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:52:49.424][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:52:49.427][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:52:49.430][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:52:49.433][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:52:49.436][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:52:49.439][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:52:49.442][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:52:49.445][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:52:49.448][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:52:49.450][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:52:49.453][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:52:49.455][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:52:49.457][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:52:49.461][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:52:49.463][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:52:49.465][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:52:49.469][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:52:49.472][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:52:49.475][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:52:49.478][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:52:49.481][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:52:49.483][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:52:49.486][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:52:49.489][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:52:49.492][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:52:49.501][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:52:49.503][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:52:49.507][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:49.509][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.512][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.544][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[2022-04-12 10:52:49.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.569][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[2022-04-12 10:52:49.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.592][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[2022-04-12 10:52:49.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:49.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:49.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:49.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:49.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:49.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:49.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:49.722][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2022-04-12 10:52:49.739][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:52:49.741][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.743][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:49.748][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.750][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2022-04-12 10:52:49.752][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.755][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:52:49.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:49.758][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.760][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2022-04-12 10:52:49.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2022-04-12 10:52:49.764][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2022-04-12 10:52:49.766][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:49.768][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:49.768][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2022-04-12 10:52:49.769][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:52:49.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:49.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:49.773][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:49.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:49.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:49.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:49.780][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-04-12 10:52:49.780][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2022-04-12 10:52:49.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:49.784][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:49.786][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:49.788][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:49.802][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:52:49.805][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:52:49.808][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:52:49.812][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:52:49.857][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:52:49.859][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2022-04-12 10:52:49.866][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:52:49.874][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:52:49.881][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:49.883][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:49.886][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2022-04-12 10:52:49.888][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2022-04-12 10:52:49.889][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-04-12 10:52:49.889][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2022-04-12 10:52:49.891][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:49.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:49.895][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2022-04-12 10:52:49.896][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2022-04-12 10:52:49.898][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:52:49.933][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:52:49.935][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:49.937][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:49.940][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:52:49.942][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:49.943][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2022-04-12 10:52:50.000][biodb::testThat]
biodb.INFO [2022-04-12 10:52:50.001][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2022-04-12 10:52:50.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:50.004][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:50.010][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2022-04-12 10:52:50.027][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:50.034][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:52:50.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:50.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:50.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:50.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:50.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:50.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:50.062][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.TRACE[2022-04-12 10:52:50.083][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:50.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:50.087][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.088][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.154][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.156][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.158][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.160][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.213][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.240][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.243][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.245][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.247][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.250][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.274][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.278][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.279][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.308][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.310][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.312][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.314][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.341][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:50.344][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:50.346][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.347][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.350][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:50.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:50.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.378][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:50.380][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:50.382][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.384][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.387][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:50.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.412][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.415][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.417][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.418][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.449][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.451][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.453][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.455][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.484][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:50.486][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:50.488][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.490][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:50.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:50.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.516][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:50.518][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:50.520][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.522][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:50.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:50.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:50.554][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:50.556][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.558][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:50.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:50.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.585][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:50.587][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:50.589][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.596][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:50.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:50.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.623][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:50.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:50.627][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.628][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:50.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:50.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.657][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:50.660][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:50.661][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.663][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.666][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:50.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.691][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:50.693][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:50.694][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.695][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.698][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:50.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.725][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:52:50.727][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:50.729][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.731][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.733][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:52:50.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:50.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:50.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:50.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.861][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.875][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.882][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.890][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:50.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:50.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:50.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.967][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:50.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:50.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:50.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:51.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:51.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:51.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.012][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:51.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.047][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:51.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:51.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:51.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:51.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:51.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:51.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.069][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:51.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:51.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:51.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:51.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:51.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:51.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:51.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:51.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:51.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.127][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:51.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:51.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:51.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:51.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:51.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:51.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.196][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.201][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.216][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:51.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:51.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:51.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:51.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.232][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:51.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:51.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.239][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:52:51.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.270][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:52:51.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:51.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.388][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.396][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.412][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:51.491][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2022-04-12 10:52:51.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:51.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:51.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.519][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:51.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:51.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:51.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:51.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:51.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:51.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.584][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.660][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.669][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:51.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.712][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.714][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.715][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.717][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:51.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:51.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.762][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.765][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.767][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.769][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:51.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.791][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.798][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.805][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.813][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.815][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.817][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.819][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.821][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:51.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.866][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.868][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:51.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.890][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.906][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.914][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.921][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.922][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.924][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.926][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.928][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:51.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.963][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.965][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.966][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.968][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:51.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.987][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:51.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:51.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:51.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:51.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:51.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.002][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:52.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:52.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.008][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:52.010][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:52.012][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.013][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.015][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:52.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:52.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:52.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:52.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:52.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:52.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:52.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.056][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:52.058][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:52.060][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.062][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:52.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:52.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.083][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.091][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.097][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.102][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.104][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.106][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.108][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.110][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.148][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.150][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.151][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.180][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.194][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.196][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.198][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.200][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.219][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.225][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.231][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.236][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.238][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.240][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.242][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.275][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.287][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.288][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.290][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.291][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.311][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:52.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:52.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.318][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:52.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:52.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:52.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:52.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.334][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:52.336][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:52.338][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.340][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:52.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:52.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:52.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:52.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:52.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:52.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:52.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.382][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:52.383][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:52.384][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.386][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:52.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.426][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.428][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.429][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.431][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.444][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.449][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.454][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.458][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.460][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.461][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.462][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.463][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.477][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:52.480][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:52.481][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.483][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.493][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.494][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.496][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.497][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.504][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.506][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.508][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.510][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:52.521][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:52.523][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.524][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.533][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:52.535][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:52.537][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.539][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.549][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.552][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:52.554][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.555][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.565][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.567][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:52.568][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.570][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.579][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.581][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:52.583][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.585][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.595][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:52.597][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:52.599][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.601][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.612][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:52.614][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:52.616][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.618][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.628][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:52.630][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:52.631][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.633][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.642][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.644][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:52.646][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.648][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.664][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:52.666][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:52.667][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.669][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.676][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:52.679][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.681][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.691][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:52.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:52.694][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.696][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.705][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:52.707][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:52.709][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.711][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.721][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:52.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:52.725][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.726][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:52.735][biodb::testThat]
biodb.INFO [2022-04-12 10:52:52.737][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-04-12 10:52:52.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:52.741][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:52.768][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2022-04-12 10:52:52.781][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-04-12 10:52:52.787][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:52.790][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-04-12 10:52:52.794][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2022-04-12 10:52:52.796][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:52.799][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2022-04-12 10:52:52.801][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:52.891][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:52.894][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:52:52.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:52.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:52.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:52.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:52.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:52.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:52.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:52.915][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:52.917][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:52.919][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.921][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.948][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.950][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.951][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.953][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.956][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:52.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.981][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.983][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.985][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.987][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:52.989][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:52.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:52.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.016][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.017][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.042][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.044][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.046][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.048][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.150][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.152][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.154][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.155][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.158][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.183][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.185][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.187][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.189][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.191][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.214][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.217][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.219][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.221][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.248][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.250][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.252][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.254][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.281][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:53.283][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:53.285][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.287][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:53.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.315][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:53.316][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:53.318][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.320][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:53.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:53.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.347][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.350][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.352][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.382][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.385][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.387][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.389][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.413][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:53.416][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:53.417][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.419][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:53.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:53.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.446][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:53.448][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:53.450][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.452][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.454][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:53.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:53.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.480][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:53.483][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:53.484][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.486][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:53.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:53.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.513][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:52:53.515][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.517][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.518][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.521][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:52:53.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:53.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:53.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:53.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.577][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:53.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:53.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:53.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:53.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.591][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:53.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:53.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:53.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:53.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.613][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:52:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:52:53.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:53.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:52:53.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:52:53.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.701][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:52:53.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:52:53.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.733][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:53.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:53.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.750][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:53.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:53.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:53.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:53.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:53.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:53.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:53.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:53.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:53.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:53.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.813][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.830][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.847][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:53.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:53.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:53.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:53.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:53.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:53.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:53.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:53.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.960][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:52:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:53.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:53.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.976][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:53.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:53.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:53.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.993][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:52:53.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:53.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.035][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:52:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:54.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.122][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:54.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.130][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:54.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:54.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.390][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:54.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:54.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:54.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:54.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.454][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2022-04-12 10:52:54.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-04-12 10:52:54.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-04-12 10:52:54.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-04-12 10:52:54.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-04-12 10:52:54.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-04-12 10:52:54.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-04-12 10:52:54.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:54.481][biodb::testThat]
biodb.INFO [2022-04-12 10:52:54.482][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2022-04-12 10:52:54.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:54.484][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:54.488][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.490][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.491][ef$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.493][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2022-04-12 10:52:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.545][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2022-04-12 10:52:54.558][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2022-04-12 10:52:54.560][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:54.561][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:54.563][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.564][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.566][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:54.568][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.569][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:54.581][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:54.583][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:54.584][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:54.585][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:52:54.587][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:52:54.588][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:52:54.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.613][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:52:54.614][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:52:54.615][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2022-04-12 10:52:54.630][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.632][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.633][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.634][ef$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.635][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2022-04-12 10:52:54.651][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.656][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.661][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.667][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[2022-04-12 10:52:54.746][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-04-12 10:52:54.748][private$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[2022-04-12 10:52:54.750][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2022-04-12 10:52:54.770][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.772][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.774][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:54.775][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.776][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:54.807][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:54.808][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:54.809][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:54.810][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:52:54.812][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:52:54.813][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:52:54.815][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.820][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.827][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:52:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:52:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.836][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:52:54.837][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:52:54.838][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2022-04-12 10:52:54.860][biodb::testThat]
biodb.INFO [2022-04-12 10:52:54.861][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2022-04-12 10:52:54.862][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:54.863][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:54.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.906][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2022-04-12 10:52:54.907][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:54.909][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:54.910][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.912][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.914][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:54.915][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:54.917][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:54.923][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:54.924][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:54.925][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:54.926][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:52:54.928][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:52:54.929][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:52:54.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:54.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:54.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:54.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:54.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:54.949][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:52:54.951][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2022-04-12 10:52:54.967][biodb::testThat]
biodb.INFO [2022-04-12 10:52:54.968][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2022-04-12 10:52:54.969][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:54.970][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:55.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:55.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.030][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.139][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:55.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:55.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:55.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:55.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:55.175][biodb::testThat]
biodb.INFO [2022-04-12 10:52:55.177][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-04-12 10:52:55.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:55.181][biodb::testThat]
biodb.INFO [2022-04-12 10:52:55.190][biodb::testThat]
biodb.INFO [2022-04-12 10:52:55.192][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-04-12 10:52:55.194][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:55.195][biodb::testThat]
biodb.INFO [2022-04-12 10:52:55.205][biodb::testThat]
biodb.INFO [2022-04-12 10:52:55.207][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2022-04-12 10:52:55.209][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:55.211][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:55.217][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2022-04-12 10:52:56.448][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2022-04-12 10:52:56.593][biodb::testThat]
biodb.INFO [2022-04-12 10:52:56.594][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2022-04-12 10:52:56.596][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:56.598][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:56.988][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.INFO [2022-04-12 10:52:57.091][biodb::testThat]
biodb.INFO [2022-04-12 10:52:57.093][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2022-04-12 10:52:57.095][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:57.097][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.221][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2022-04-12 10:52:57.223][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:57.225][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:57.229][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:57.232][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:57.235][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:57.238][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:57.240][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:57.275][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:57.277][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:57.278][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:57.280][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:52:57.281][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:52:57.283][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:52:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.315][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:52:57.316][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:52:57.334][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2022-04-12 10:52:57.336][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:57.338][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2022-04-12 10:52:57.340][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:57.343][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:57.345][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:57.347][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:57.349][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:57.358][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:57.359][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:57.360][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:57.362][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:52:57.363][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:52:57.364][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:52:57.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.400][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:52:57.401][private$doSearchForEntries] COUNT IDS = 1
biodb.TRACE[2022-04-12 10:52:57.418][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.422][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.427][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.437][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.WARN [2022-04-12 10:52:57.457][self$searchForEntries] This database is not searchable by field "average.mass".
biodb.TRACE[2022-04-12 10:52:57.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.WARN [2022-04-12 10:52:57.529][self$searchForEntries] This database is not searchable by field "monoisotopic.mass".
biodb.TRACE[2022-04-12 10:52:57.534][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:57.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:57.551][biodb::testThat]
biodb.INFO [2022-04-12 10:52:57.553][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-04-12 10:52:57.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:57.557][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.569][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.577][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.585][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:57.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:57.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:57.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:57.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:57.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:57.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:57.606][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.WARN [2022-04-12 10:52:57.735][self$searchForEntries] This database is not searchable by field "average.mass".
biodb.TRACE[2022-04-12 10:52:57.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:57.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:57.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:57.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:57.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:57.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:57.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2022-04-12 10:52:57.979][self$searchForEntries] This database is not searchable by field "monoisotopic.mass".
biodb.TRACE[2022-04-12 10:52:58.016][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:58.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:58.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:58.022][biodb::testThat]
biodb.INFO [2022-04-12 10:52:58.023][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-04-12 10:52:58.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:58.025][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:58.029][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.037][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.044][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.051][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:58.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:58.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:58.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:58.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:58.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:58.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:58.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2022-04-12 10:52:58.184][self$searchForEntries] This database is not searchable by field "average.mass".
biodb.TRACE[2022-04-12 10:52:58.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:58.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:58.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:58.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:58.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:58.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:58.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:58.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:58.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:58.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2022-04-12 10:52:58.334][self$searchForEntries] This database is not searchable by field "monoisotopic.mass".
biodb.TRACE[2022-04-12 10:52:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:58.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:58.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:58.350][biodb::testThat]
biodb.INFO [2022-04-12 10:52:58.351][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-04-12 10:52:58.353][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:58.354][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:58.359][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.366][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.377][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:58.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:58.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:58.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:58.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:58.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:58.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:58.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2022-04-12 10:52:58.523][self$searchForEntries] This database is not searchable by field "average.mass".
biodb.TRACE[2022-04-12 10:52:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:58.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:58.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:58.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:58.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:58.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:58.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:58.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:58.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:58.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2022-04-12 10:52:58.712][self$searchForEntries] This database is not searchable by field "monoisotopic.mass".
biodb.TRACE[2022-04-12 10:52:58.718][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:58.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:52:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:58.725][biodb::testThat]
biodb.INFO [2022-04-12 10:52:58.727][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2022-04-12 10:52:58.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:58.730][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:58.734][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-04-12 10:52:58.822][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-04-12 10:52:58.826][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:58.828][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-04-12 10:52:58.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-04-12 10:52:58.867][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:52:58.869][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:52:58.871][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:58.874][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:58.930][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:58.932][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:52:58.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:58.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:58.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:58.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:58.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:58.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:58.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:58.952][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.960][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:58.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:58.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:58.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:58.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:58.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:58.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:59.012][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-04-12 10:52:59.014][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.INFO [2022-04-12 10:52:59.044][biodb::testThat]
biodb.INFO [2022-04-12 10:52:59.045][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-04-12 10:52:59.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:59.049][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:59.065][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2022-04-12 10:52:59.067][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2022-04-12 10:52:59.069][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-04-12 10:52:59.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.074][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-04-12 10:52:59.078][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2022-04-12 10:52:59.080][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:52:59.082][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:52:59.084][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:59.086][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.132][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:59.134][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:52:59.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:59.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:59.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:59.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.143][FUN] Functions in observer BiodbConfig: [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[2022-04-12 10:52:59.145][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:59.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:59.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.150][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:59.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:52:59.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:59.186][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-04-12 10:52:59.188][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.DEBUG[2022-04-12 10:52:59.190][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2022-04-12 10:52:59.212][biodb::testThat]
biodb.INFO [2022-04-12 10:52:59.214][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2022-04-12 10:52:59.216][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:59.218][biodb::testThat]
biodb.INFO [2022-04-12 10:52:59.264][biodb::testThat]
biodb.INFO [2022-04-12 10:52:59.266][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2022-04-12 10:52:59.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:59.269][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:59.273][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.276][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.278][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:59.280][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.281][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:59.302][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:59.303][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:59.305][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:59.307][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2022-04-12 10:52:59.318][biodb::testThat]
biodb.INFO [2022-04-12 10:52:59.320][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2022-04-12 10:52:59.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:59.323][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:59.326][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.328][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.331][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:52:59.333][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:52:59.335][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:52:59.352][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:52:59.354][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:52:59.355][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:52:59.356][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2022-04-12 10:52:59.367][biodb::testThat]
biodb.INFO [2022-04-12 10:52:59.370][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2022-04-12 10:52:59.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:59.373][biodb::testThat]
biodb.ERROR[2022-04-12 10:52:59.396][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-04-12 10:52:59.423][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-04-12 10:52:59.434][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:52:59.436][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2022-04-12 10:52:59.445][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2022-04-12 10:52:59.447][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:52:59.448][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:59.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:59.450][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.452][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.453][FUN] Functions in observer BiodbConfig: [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 [2022-04-12 10:52:59.457][biodb::testContext]
biodb.INFO [2022-04-12 10:52:59.458][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:59.459][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2022-04-12 10:52:59.460][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:59.462][biodb::testContext]
biodb.INFO [2022-04-12 10:52:59.477][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:52:59.479][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:52:59.483][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:59.485][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:52:59.486][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:52:59.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.490][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:52:59.491][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:52:59.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.498][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:52:59.500][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:52:59.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.507][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:52:59.509][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:52:59.511][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:52:59.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.516][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:52:59.517][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:52:59.518][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:52:59.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.522][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:52:59.524][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:52:59.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.538][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:52:59.540][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:52:59.542][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:52:59.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.550][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:52:59.552][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:52:59.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.560][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:52:59.561][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:52:59.562][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:52:59.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.568][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:52:59.570][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:52:59.572][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:52:59.574][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:52:59.577][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:52:59.579][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:52:59.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.585][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:52:59.587][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:52:59.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.595][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:52:59.597][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:52:59.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.604][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:52:59.607][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:52:59.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.615][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:52:59.617][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:52:59.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.624][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:52:59.626][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:52:59.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.634][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:52:59.636][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:52:59.648][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:52:59.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.656][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:52:59.658][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:52:59.660][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:52:59.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.668][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:52:59.672][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.674][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:52:59.676][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.678][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:59.681][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.683][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.685][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.690][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:52:59.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:59.694][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.696][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:52:59.698][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:59.701][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:59.705][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:59.705][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:59.705][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:52:59.705][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:52:59.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:59.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.713][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:59.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.721][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:59.726][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:59.728][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.730][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.732][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:52:59.735][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.737][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:52:59.739][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.742][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:59.744][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.746][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.750][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.752][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:52:59.755][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:59.757][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.759][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:52:59.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:59.763][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.767][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:59.767][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:59.767][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:59.767][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:52:59.767][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:52:59.769][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:59.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.773][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:59.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.783][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.785][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:59.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:59.790][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.792][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.794][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:52:59.798][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.801][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:52:59.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:59.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.809][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.811][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.813][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.816][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:52:59.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:59.820][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.822][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:52:59.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:59.826][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.828][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.830][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.831][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:59.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:59.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.840][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.842][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:59.846][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:59.848][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.850][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.852][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:52:59.856][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.858][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:52:59.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.863][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:59.865][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.873][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:52:59.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:59.877][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.879][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:52:59.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:59.883][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.885][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:59.887][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.888][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:59.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.894][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:59.896][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:59.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:59.900][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:59.902][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.903][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:59.904][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:59.906][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:59.916][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:59.919][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:59.921][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:59.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.057][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[2022-04-12 10:53:00.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.068][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:53:00.071][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:53:00.074][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:53:00.077][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:53:00.080][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:00.083][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:00.086][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:00.089][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:00.092][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:53:00.095][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:00.098][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:00.101][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:53:00.104][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:00.107][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:00.110][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:53:00.113][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:00.116][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:53:00.119][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:53:00.122][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:00.125][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:53:00.127][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:53:00.130][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:53:00.134][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:53:00.137][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:53:00.140][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:53:00.143][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:53:00.147][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:53:00.151][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:53:00.154][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:53:00.157][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:53:00.160][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:53:00.162][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:53:00.164][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:53:00.167][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:53:00.171][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:53:00.174][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:53:00.176][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:53:00.178][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:53:00.180][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:53:00.181][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:53:00.183][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:53:00.186][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:53:00.189][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:53:00.191][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:53:00.194][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:53:00.197][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:53:00.199][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:53:00.201][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:53:00.204][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:53:00.207][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:53:00.210][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:53:00.213][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:53:00.216][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:53:00.219][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:53:00.222][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:53:00.226][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:53:00.228][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:53:00.232][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:53:00.235][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:53:00.238][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:53:00.241][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:53:00.243][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:53:00.245][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:53:00.247][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:53:00.248][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:53:00.250][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:53:00.252][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:00.283][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:00.285][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:53:00.287][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:53:00.290][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:53:00.293][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:53:00.296][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:53:00.298][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:53:00.300][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:53:00.303][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:53:00.306][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:53:00.309][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:53:00.312][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:53:00.316][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:53:00.319][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:53:00.322][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:53:00.325][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:53:00.328][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:53:00.331][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:00.334][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:00.336][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.339][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.340][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[2022-04-12 10:53:00.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.368][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[2022-04-12 10:53:00.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.378][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[2022-04-12 10:53:00.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:00.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.524][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:00.527][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:00.531][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:00.533][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:53:00.536][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:00.538][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:00.541][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:00.543][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2022-04-12 10:53:00.545][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:00.547][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:00.549][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:53:00.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:00.553][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:00.555][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2022-04-12 10:53:00.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2022-04-12 10:53:00.560][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2022-04-12 10:53:00.562][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:00.565][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:00.565][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2022-04-12 10:53:00.567][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:53:00.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:00.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:00.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:00.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:00.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:00.580][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:00.582][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-04-12 10:53:00.582][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2022-04-12 10:53:00.585][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:00.586][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:00.588][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:00.590][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:00.592][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:00.596][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:00.599][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:00.602][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:00.608][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:00.610][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2022-04-12 10:53:00.612][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:00.616][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:53:00.626][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:00.629][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:00.631][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2022-04-12 10:53:00.633][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2022-04-12 10:53:00.635][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-04-12 10:53:00.635][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2022-04-12 10:53:00.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:00.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:00.639][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2022-04-12 10:53:00.641][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2022-04-12 10:53:00.643][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:00.646][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:53:00.649][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:00.651][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:00.653][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:53:00.655][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:00.657][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2022-04-12 10:53:00.659][biodb::testThat]
biodb.INFO [2022-04-12 10:53:00.661][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2022-04-12 10:53:00.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:00.664][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:00.671][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:00.673][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:00.676][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:53:00.679][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:00.681][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:53:00.700][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:53:00.702][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:53:00.704][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:53:00.706][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:53:00.711][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2022-04-12 10:53:00.716][biodb::testThat]
biodb.INFO [2022-04-12 10:53:00.718][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2022-04-12 10:53:00.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:00.722][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:00.726][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2022-04-12 10:53:00.729][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-04-12 10:53:00.732][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:00.735][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-04-12 10:53:00.739][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2022-04-12 10:53:00.742][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:00.747][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2022-04-12 10:53:00.749][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:00.791][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:00.792][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:53:00.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:00.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.805][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.TRACE[2022-04-12 10:53:00.811][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.813][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.815][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.817][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.841][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:00.842][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:00.843][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.845][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.847][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:00.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:00.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.868][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:00.870][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:00.872][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.874][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.876][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:00.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:00.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.901][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.904][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.906][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.908][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.932][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:00.934][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:00.936][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.938][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:00.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:00.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.965][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:00.967][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:00.969][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.979][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.981][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:00.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.004][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.006][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.008][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.010][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.012][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.037][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.040][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.041][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.043][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.071][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.073][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.077][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.100][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.102][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.103][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.104][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.106][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.130][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.132][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.134][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.136][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.162][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.164][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.166][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.167][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.192][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.195][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.197][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.198][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.226][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.228][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.230][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.232][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.256][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:01.258][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:01.260][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.261][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.262][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:01.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:01.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.282][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:01.284][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:01.285][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.286][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.288][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:01.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.320][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:53:01.322][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.324][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.326][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.328][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:53:01.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.371][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:01.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.378][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:01.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:01.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.385][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:01.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:01.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.391][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:01.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:01.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.399][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:01.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:01.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.406][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:01.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:01.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:01.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:01.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:01.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:01.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:01.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:01.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:01.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:01.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:01.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:01.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:01.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:01.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:01.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:01.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.522][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.530][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:01.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:01.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:01.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.550][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.606][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:01.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:01.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.612][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:01.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:01.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.619][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:01.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:01.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:01.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.686][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:01.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.701][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:01.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:01.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.709][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:01.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:01.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.717][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:01.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:01.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.725][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:53:01.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.751][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:53:01.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.813][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:01.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:01.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.819][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:01.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:01.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.829][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:01.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:01.894][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2022-04-12 10:53:01.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:01.924][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:53:01.926][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2022-04-12 10:53:01.928][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2022-04-12 10:53:01.929][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:53:01.930][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:01.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:01.934][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:01.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:01.936][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:01.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 10:53:01.942][biodb::testContext]
biodb.INFO [2022-04-12 10:53:01.944][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:01.946][biodb::testContext] Test context - Test search of entries
biodb.INFO [2022-04-12 10:53:01.948][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:01.950][biodb::testContext]
biodb.INFO [2022-04-12 10:53:01.981][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:01.984][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:01.993][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:01.995][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:53:01.997][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:53:01.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.003][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:53:02.005][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:53:02.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.013][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:53:02.015][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:53:02.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.020][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:53:02.022][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:53:02.024][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:53:02.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.031][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:53:02.033][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:53:02.035][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:53:02.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.041][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:53:02.042][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:53:02.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.048][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:53:02.050][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:53:02.053][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:53:02.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.060][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:53:02.062][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:53:02.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.069][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:53:02.070][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:53:02.071][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:53:02.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.075][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:02.077][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:53:02.078][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:53:02.079][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:53:02.080][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:53:02.081][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:53:02.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.086][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:53:02.087][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:53:02.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.092][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:53:02.093][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:53:02.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.100][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:53:02.102][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:53:02.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.107][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[2022-04-12 10:53:02.108][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:53:02.110][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:53:02.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.114][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:53:02.116][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:53:02.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.120][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:02.122][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:53:02.134][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:53:02.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.141][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:53:02.142][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:53:02.145][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:53:02.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.151][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:53:02.154][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.155][self$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[2022-04-12 10:53:02.157][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.158][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:02.159][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.161][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.165][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.167][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:02.169][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:02.171][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.173][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:53:02.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:02.176][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.178][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.180][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:02.180][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:02.180][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:02.180][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:02.180][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:02.182][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:02.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:02.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.194][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.196][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:02.197][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:02.199][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.201][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.203][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:53:02.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.209][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:02.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:02.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.217][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.220][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:02.222][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:02.224][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.225][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:53:02.228][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:02.230][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.232][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.234][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:02.234][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:02.234][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:02.234][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:02.234][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:02.236][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:02.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.241][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:02.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.247][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.249][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:02.253][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:02.254][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.256][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.259][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:53:02.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.263][self$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[2022-04-12 10:53:02.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:02.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.268][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.269][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.271][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.272][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:02.274][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:02.277][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.279][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:53:02.281][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:02.283][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.292][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.294][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.295][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:02.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.298][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:02.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.302][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:02.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:02.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.307][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.308][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:53:02.310][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.311][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:02.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:02.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.316][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.317][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.319][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:02.320][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:02.321][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.322][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:53:02.324][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:02.325][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.326][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.327][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.328][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:02.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.331][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:02.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.335][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.336][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.337][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:02.338][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:02.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.340][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.342][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:02.343][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.354][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[2022-04-12 10:53:02.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.359][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[2022-04-12 10:53:02.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.364][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[2022-04-12 10:53:02.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.394][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[2022-04-12 10:53:02.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.399][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[2022-04-12 10:53:02.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.431][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:53:02.433][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:53:02.435][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:53:02.437][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:53:02.438][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:02.440][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:02.442][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:02.443][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:02.445][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:53:02.446][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:02.448][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:02.450][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:53:02.451][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:02.453][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:02.455][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:53:02.456][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:02.458][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:53:02.459][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:53:02.461][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:02.463][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:53:02.464][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:53:02.466][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:53:02.468][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:53:02.469][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:53:02.471][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:53:02.473][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:53:02.474][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:53:02.476][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:53:02.478][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:53:02.479][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:53:02.481][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:53:02.482][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:53:02.484][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:53:02.486][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:53:02.487][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:53:02.489][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:53:02.490][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:53:02.492][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:53:02.499][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:53:02.501][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:53:02.502][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:53:02.504][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:53:02.506][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:53:02.507][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:53:02.509][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:53:02.512][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:53:02.515][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:53:02.518][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:53:02.519][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:53:02.521][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:53:02.523][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:53:02.524][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:53:02.526][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:53:02.528][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:53:02.529][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:53:02.532][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:53:02.535][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:53:02.538][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:53:02.540][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:53:02.543][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:53:02.546][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:53:02.548][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:53:02.551][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:53:02.553][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:53:02.556][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:53:02.559][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:53:02.561][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:02.563][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:02.565][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:53:02.566][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:53:02.568][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:53:02.571][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:53:02.574][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:53:02.577][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:53:02.580][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:53:02.581][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:53:02.583][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:53:02.585][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:53:02.588][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:53:02.591][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:53:02.593][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:53:02.595][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:53:02.596][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:53:02.598][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:53:02.600][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:02.601][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:02.603][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.607][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.758][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[2022-04-12 10:53:02.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:02.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.800][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:02.803][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:02.807][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.809][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:02.814][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.816][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2022-04-12 10:53:02.818][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.822][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:53:02.824][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:02.826][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.828][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2022-04-12 10:53:02.830][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2022-04-12 10:53:02.832][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2022-04-12 10:53:02.835][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:02.837][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:02.837][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2022-04-12 10:53:02.839][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:53:02.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.844][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:02.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:02.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:02.850][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:02.852][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-04-12 10:53:02.852][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2022-04-12 10:53:02.855][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:02.857][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:02.859][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:02.861][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:02.862][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:02.865][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:02.869][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:02.872][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:02.879][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:02.880][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2022-04-12 10:53:02.883][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:02.886][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:53:02.888][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:02.890][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:02.893][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2022-04-12 10:53:02.895][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2022-04-12 10:53:02.897][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2022-04-12 10:53:02.897][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2022-04-12 10:53:02.900][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:02.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:02.903][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2022-04-12 10:53:02.905][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2022-04-12 10:53:02.907][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2022-04-12 10:53:02.910][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:53:02.913][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:02.915][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:02.918][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2022-04-12 10:53:02.920][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:02.923][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2022-04-12 10:53:02.925][biodb::testThat]
biodb.INFO [2022-04-12 10:53:02.927][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2022-04-12 10:53:02.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:02.932][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:02.951][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-04-12 10:53:02.953][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2022-04-12 10:53:02.955][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2022-04-12 10:53:02.960][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:02.963][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:02.966][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:53:02.969][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:02.971][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:53:02.993][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:53:02.996][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:53:02.997][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:53:02.999][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:53:03.001][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:53:03.003][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2022-04-12 10:53:03.006][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2022-04-12 10:53:03.008][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-04-12 10:53:03.012][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:03.015][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-04-12 10:53:03.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2022-04-12 10:53:03.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:03.025][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2022-04-12 10:53:03.028][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:03.077][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:03.080][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:53:03.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:03.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:03.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:03.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:03.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:03.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:03.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:03.101][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.105][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.107][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.135][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.137][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.139][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.141][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.144][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.180][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.182][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.184][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.186][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.189][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.217][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.219][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.220][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.249][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.251][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.252][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.254][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.282][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.284][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.286][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.288][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.291][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.318][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:03.320][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:03.322][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.325][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.327][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:03.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:03.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.355][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.357][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.359][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.361][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.387][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.390][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.392][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.394][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.424][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.428][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.430][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.461][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.465][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.466][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.491][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.493][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.495][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.497][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.527][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.531][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.532][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.567][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:03.568][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:03.570][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.571][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:03.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.597][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:03.599][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:03.600][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.602][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.604][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:03.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:03.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.630][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:03.633][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:03.635][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.637][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.638][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:03.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.665][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:53:03.667][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.669][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.671][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.674][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:53:03.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.725][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.732][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.737][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:03.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.744][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.752][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.759][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:03.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:03.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.824][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:03.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.839][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.847][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:03.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.881][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:03.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:03.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.898][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:03.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:03.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.906][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:03.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:03.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.954][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.962][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.969][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.977][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:04.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:04.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.028][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.036][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.043][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.051][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:04.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:04.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:04.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:04.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.067][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:04.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:04.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:53:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:53:04.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.182][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:04.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:04.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.190][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:04.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:04.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.205][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:04.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:04.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:04.280][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2022-04-12 10:53:04.282][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:04.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.288][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:04.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:04.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.296][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:04.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:04.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.303][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:04.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:04.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:04.310][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:53:04.311][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:53:04.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:04.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:04.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:04.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:04.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:04.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:04.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:04.326][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2022-04-12 10:53:04.328][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2022-04-12 10:53:04.331][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:04.333][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2022-04-12 10:53:04.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2022-04-12 10:53:04.340][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:04.343][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2022-04-12 10:53:04.345][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:04.386][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:04.388][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2022-04-12 10:53:04.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:04.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:04.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:04.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:04.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:04.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:04.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:04.409][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.415][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.444][ef$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.446][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.448][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.450][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.453][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.480][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:04.482][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:04.484][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.486][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.489][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:04.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:04.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:04.512][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:04.514][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.516][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:04.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.542][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:04.544][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:04.545][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.546][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:04.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.581][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:04.583][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:04.585][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.586][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.589][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:04.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:04.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.613][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.615][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.616][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.617][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.640][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:04.641][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:04.642][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.643][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:04.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.661][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:04.663][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:04.664][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.665][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:04.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:04.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.689][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:04.691][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:04.693][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.695][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:04.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:04.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.725][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:04.727][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:04.729][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.730][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:04.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.757][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.759][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.760][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.762][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:04.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.788][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:04.790][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:04.792][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.794][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:04.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:04.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.823][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.828][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.830][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:04.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.855][ef$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:04.857][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:04.858][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.859][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.861][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:04.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:04.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.887][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:04.889][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:04.890][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.891][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:04.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:04.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.918][ef$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:53:04.920][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:04.922][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.924][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.926][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2022-04-12 10:53:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:04.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:04.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.978][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.987][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:04.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:04.995][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:04.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:05.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:05.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.013][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:05.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:05.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-04-12 10:53:05.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-04-12 10:53:05.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:05.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:05.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:05.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:05.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:05.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2022-04-12 10:53:05.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.075][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:05.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:05.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:05.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:05.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:05.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.101][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:05.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:05.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:05.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:05.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2022-04-12 10:53:05.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:05.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:05.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.124][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:05.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:05.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:05.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2022-04-12 10:53:05.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.141][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.149][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.158][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:05.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:05.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:05.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:05.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:05.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:05.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:05.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:05.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:05.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:05.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:05.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:05.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.262][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.271][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:05.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:05.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.338][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:05.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:05.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:05.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:05.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:05.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:05.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.370][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:05.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.376][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:53:05.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.400][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2022-04-12 10:53:05.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.488][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:05.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:05.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.496][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:05.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:05.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.513][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:05.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:05.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.591][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2022-04-12 10:53:05.593][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.610][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.618][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.625][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.631][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:53:05.632][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:53:05.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:05.644][function(conn)] Found ids when searching for words "[1]: "and"": [2]: "HMDB0000001, HMDB0000002".
biodb.DEBUG[2022-04-12 10:53:05.661][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-04-12 10:53:05.662][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2022-04-12 10:53:05.663][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2022-04-12 10:53:05.665][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:05.667][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:05.669][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:53:05.671][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:05.672][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:53:05.686][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:53:05.687][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:53:05.688][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:53:05.690][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:53:05.691][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:53:05.692][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:53:05.694][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.700][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.705][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.729][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:53:05.730][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:53:05.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.742][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.TRACE[2022-04-12 10:53:05.744][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.760][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.768][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.780][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.788][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.795][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2022-04-12 10:53:05.797][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:53:05.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:05.812][function(conn)] Found ids when searching for words "[2]: "histidine, cerebrovascular"": [1]: "HMDB0000001".
biodb.DEBUG[2022-04-12 10:53:05.836][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2022-04-12 10:53:05.838][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2022-04-12 10:53:05.840][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2022-04-12 10:53:05.843][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:05.846][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:05.849][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2022-04-12 10:53:05.852][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2022-04-12 10:53:05.854][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2022-04-12 10:53:05.876][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2022-04-12 10:53:05.878][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2022-04-12 10:53:05.880][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2022-04-12 10:53:05.882][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2022-04-12 10:53:05.884][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2022-04-12 10:53:05.886][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2022-04-12 10:53:05.889][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.898][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.916][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.925][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.931][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.939][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.947][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.956][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2022-04-12 10:53:05.958][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2022-04-12 10:53:05.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.973][FUN] Functions in observer BiodbConfig: [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[2022-04-12 10:53:05.976][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.991][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:05.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:05.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.999][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:06.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:06.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:06.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:06.008][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:06.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:06.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:06.017][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:06.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:06.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:06.024][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-04-12 10:53:06.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-04-12 10:53:06.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:06.032][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2022-04-12 10:53:06.034][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2022-04-12 10:53:06.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:06.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:06.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:06.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:06.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:06.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:06.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:06.049][function(conn)] Found ids when searching for words "[2]: "monoalkylamines, shiitakes"": [1]: "HMDB0000002".
biodb.INFO [2022-04-12 10:53:06.056][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:53:06.059][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2022-04-12 10:53:06.061][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2022-04-12 10:53:06.062][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:53:06.063][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:06.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:06.066][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:06.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:06.070][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:06.072][FUN] Functions in observer 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 230 ]
>
> proc.time()
user system elapsed
18.898 0.606 21.248
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 2.913 | 0.604 | 3.639 | |
| HmdbMetabolitesEntry | 0.511 | 0.014 | 0.527 | |