Pierrick Roger
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: devel |
| git_last_commit: d2b9830 |
| git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-15 11:39 -0500 (Sat, 15 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 203/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbHmdb |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz |
| StartedAt: 2025-02-14 20:10:37 -0500 (Fri, 14 Feb 2025) |
| EndedAt: 2025-02-14 20:11:30 -0500 (Fri, 14 Feb 2025) |
| EllapsedTime: 53.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘biodbHmdb’ ... ** this is package ‘biodbHmdb’ version ‘1.13.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c EntryMaker.cpp -o EntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c FileEntryMaker.cpp -o FileEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c TagDetector.cpp -o TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c XmlSplitter.cpp -o XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-100-TagDetector.cpp -o test-100-TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help No man pages found in package ‘biodbHmdb’ *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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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 [2025-02-14 20:11:10.292][biodb::testContext]
biodb.INFO [2025-02-14 20:11:10.295][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:10.296][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-02-14 20:11:10.297][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:10.298][biodb::testContext]
biodb.INFO [2025-02-14 20:11:10.299][biodb::testThat]
biodb.INFO [2025-02-14 20:11:10.300][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2025-02-14 20:11:10.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:10.302][biodb::testThat]
biodb.INFO [2025-02-14 20:11:10.391][biodb::testContext]
biodb.INFO [2025-02-14 20:11:10.392][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:10.393][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-02-14 20:11:10.394][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:10.395][biodb::testContext]
biodb.INFO [2025-02-14 20:11:10.403][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-14 20:11:10.404][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-14 20:11:10.411][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:10.412][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-14 20:11:10.413][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-14 20:11:10.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.416][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-14 20:11:10.440][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-14 20:11:10.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.443][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[2025-02-14 20:11:10.444][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-14 20:11:10.445][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-14 20:11:10.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.448][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-14 20:11:10.449][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-14 20:11:10.450][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-14 20:11:10.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.453][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.DEBUG[2025-02-14 20:11:10.454][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-14 20:11:10.454][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-14 20:11:10.455][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-14 20:11:10.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.465][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-14 20:11:10.467][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-14 20:11:10.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.472][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-14 20:11:10.473][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-14 20:11:10.474][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-14 20:11:10.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.478][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-14 20:11:10.479][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-14 20:11:10.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.483][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-14 20:11:10.484][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-14 20:11:10.485][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-14 20:11:10.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.489][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-14 20:11:10.490][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-14 20:11:10.491][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-14 20:11:10.493][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-14 20:11:10.494][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-14 20:11:10.495][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-14 20:11:10.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.499][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-14 20:11:10.500][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-14 20:11:10.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.504][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-14 20:11:10.505][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-14 20:11:10.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.509][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-14 20:11:10.510][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-14 20:11:10.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.514][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-14 20:11:10.515][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-14 20:11:10.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.519][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-14 20:11:10.520][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-14 20:11:10.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.524][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-14 20:11:10.525][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-14 20:11:10.529][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-14 20:11:10.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.533][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-14 20:11:10.534][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-14 20:11:10.535][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-14 20:11:10.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.543][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-14 20:11:10.582][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.601][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-14 20:11:10.602][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.603][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:10.604][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.609][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-14 20:11:10.610][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:10.611][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.612][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-14 20:11:10.613][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:10.614][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.616][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:10.616][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-14 20:11:10.616][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-14 20:11:10.616][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-14 20:11:10.616][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-14 20:11:10.617][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:10.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:10.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.635][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:10.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:10.638][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.639][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.640][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-14 20:11:10.642][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.643][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-14 20:11:10.645][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.646][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:10.647][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.649][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.650][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.651][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-14 20:11:10.652][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:10.653][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.654][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-14 20:11:10.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:10.656][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.658][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:10.658][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-14 20:11:10.658][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-14 20:11:10.658][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-14 20:11:10.658][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-14 20:11:10.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:10.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:10.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.665][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.666][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.667][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:10.668][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:10.669][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.670][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.671][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-14 20:11:10.673][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.674][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-14 20:11:10.675][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.676][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:10.677][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.679][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.680][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.681][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-14 20:11:10.682][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:10.683][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.684][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-14 20:11:10.685][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:10.685][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.686][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.687][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.688][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:10.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:10.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.694][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.695][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.696][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:10.697][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:10.697][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.698][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.699][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-14 20:11:10.701][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.702][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-14 20:11:10.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.704][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:10.705][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.706][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.707][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.708][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.709][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-14 20:11:10.710][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:10.711][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.712][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-14 20:11:10.713][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:10.714][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.715][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:10.716][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.716][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:10.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.719][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:10.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:10.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:10.722][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:10.723][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:10.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:10.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:10.726][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:10.730][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:10.731][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.758][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[2025-02-14 20:11:10.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.806][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-14 20:11:10.816][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-14 20:11:10.817][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-14 20:11:10.818][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-14 20:11:10.820][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-14 20:11:10.821][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-14 20:11:10.822][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-14 20:11:10.824][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-14 20:11:10.825][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-14 20:11:10.826][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-14 20:11:10.827][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-14 20:11:10.829][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-14 20:11:10.830][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-14 20:11:10.831][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-14 20:11:10.833][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-14 20:11:10.834][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-14 20:11:10.835][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-14 20:11:10.836][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-14 20:11:10.838][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-14 20:11:10.839][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-14 20:11:10.840][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-14 20:11:10.842][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-14 20:11:10.843][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-14 20:11:10.844][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-14 20:11:10.845][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-14 20:11:10.847][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-14 20:11:10.848][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-14 20:11:10.849][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-14 20:11:10.851][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-14 20:11:10.852][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-14 20:11:10.853][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-14 20:11:10.855][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-14 20:11:10.856][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-14 20:11:10.857][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-14 20:11:10.859][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-14 20:11:10.860][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-14 20:11:10.861][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-14 20:11:10.862][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-14 20:11:10.864][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-14 20:11:10.865][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-14 20:11:10.866][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-14 20:11:10.868][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-14 20:11:10.869][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-14 20:11:10.870][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-14 20:11:10.872][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-14 20:11:10.873][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-14 20:11:10.874][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-14 20:11:10.876][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-14 20:11:10.877][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-14 20:11:10.878][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-14 20:11:10.880][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-14 20:11:10.881][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-14 20:11:10.882][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-14 20:11:10.884][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-14 20:11:10.885][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-14 20:11:10.886][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-14 20:11:10.888][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-14 20:11:10.889][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-14 20:11:10.890][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-14 20:11:10.892][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-14 20:11:10.893][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-14 20:11:10.894][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-14 20:11:10.896][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-14 20:11:10.897][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-14 20:11:10.898][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-14 20:11:10.901][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-14 20:11:10.903][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-14 20:11:10.904][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-14 20:11:10.905][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-14 20:11:10.907][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-14 20:11:10.908][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-14 20:11:10.909][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-14 20:11:10.911][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-14 20:11:10.912][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-14 20:11:10.914][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-14 20:11:10.915][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-14 20:11:10.917][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-14 20:11:10.918][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-14 20:11:10.919][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-14 20:11:10.921][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-14 20:11:10.922][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-14 20:11:10.924][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-14 20:11:10.925][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-14 20:11:10.931][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-14 20:11:10.933][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-14 20:11:10.936][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:10.937][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.938][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:10.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:10.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.949][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.DEBUG[2025-02-14 20:11:10.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:10.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:10.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:10.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:10.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.961][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[2025-02-14 20:11:10.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:10.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:10.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:10.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:10.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:10.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:10.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:10.973][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.DEBUG[2025-02-14 20:11:10.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:10.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:10.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:10.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:10.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.031][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[2025-02-14 20:11:11.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:11.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.066][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[2025-02-14 20:11:11.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:11.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.072][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.DEBUG[2025-02-14 20:11:11.074][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-14 20:11:11.083][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:11.085][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:11.086][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-14 20:11:11.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:11.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:11.089][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:11.090][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-14 20:11:11.091][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:11.092][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:11.093][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-14 20:11:11.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:11.095][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:11.096][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-14 20:11:11.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-14 20:11:11.098][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-14 20:11:11.099][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:11.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:11.100][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-14 20:11:11.100][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-14 20:11:11.101][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-14 20:11:11.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:11.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:11.104][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:11.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:11.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:11.106][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:11.107][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-14 20:11:11.107][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-14 20:11:11.108][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:11.109][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:11.110][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:11.111][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:11.117][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-14 20:11:11.118][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-14 20:11:11.120][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-14 20:11:11.121][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-14 20:11:11.122][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-14 20:11:11.144][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:11.145][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-14 20:11:11.149][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:11.153][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:11.157][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:11.158][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:11.159][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-14 20:11:11.160][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-02-14 20:11:11.161][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-14 20:11:11.161][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-02-14 20:11:11.162][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:11.163][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:11.164][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-02-14 20:11:11.165][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-02-14 20:11:11.166][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:11.189][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:11.190][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:11.191][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:11.192][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:11.193][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:11.194][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-02-14 20:11:11.202][biodb::testThat]
biodb.INFO [2025-02-14 20:11:11.203][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-02-14 20:11:11.204][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:11.205][biodb::testThat]
biodb.TRACE[2025-02-14 20:11:11.208][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-02-14 20:11:11.210][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:11.213][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:11.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:11.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:11.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:11.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:11.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:11.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:11.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:11.240][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.241][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.243][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.260][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.261][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.263][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.292][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.293][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.295][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.296][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.300][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.301][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.303][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.304][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.308][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.309][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.311][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.316][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.317][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.319][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.324][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.326][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.327][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.339][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.340][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.342][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.347][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.348][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.350][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.355][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.356][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.358][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.363][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:11.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:11.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.366][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:11.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:11.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.371][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:11.372][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:11.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.374][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:11.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:11.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.379][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.380][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.382][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.387][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.388][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.390][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.395][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.396][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.398][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.403][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:11.404][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:11.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.406][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.407][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:11.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.411][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:11.412][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:11.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.414][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.415][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:11.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:11.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.419][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:11.420][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.422][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.423][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:11.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.474][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.478][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.482][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:11.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.486][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.489][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.493][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:11.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:11.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:11.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:11.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.555][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:11.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:11.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.559][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:11.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:11.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.562][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:11.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:11.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:11.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:11.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.570][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:11.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:11.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.574][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:11.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:11.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:11.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:11.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:11.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:11.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:11.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:11.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.600][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.604][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.608][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:11.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:11.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.640][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.643][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.651][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.655][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.659][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.663][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:11.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:11.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:11.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:11.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:11.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:11.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.674][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:11.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.689][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:11.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:11.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:11.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:11.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.731][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.735][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.743][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:11.774][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-14 20:11:11.777][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-14 20:11:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-14 20:11:11.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.780][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-14 20:11:11.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-14 20:11:11.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.784][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-14 20:11:11.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-14 20:11:11.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-14 20:11:11.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-14 20:11:11.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.815][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.848][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.851][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.855][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:11.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.878][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.879][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.893][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.896][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.905][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.909][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.910][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.912][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:11.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.935][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.936][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.938][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:11.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.958][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.962][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.963][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.964][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.991][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:11.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:11.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:11.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.002][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.006][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.010][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.014][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.015][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.016][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.017][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.044][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.047][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.058][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.066][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.070][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.071][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.073][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.074][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.096][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.099][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.111][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.119][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.123][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.124][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.125][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.149][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.150][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.152][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.175][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.176][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.178][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.205][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.206][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.208][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.224][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.228][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.232][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.233][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.235][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.236][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.247][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.251][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.259][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.260][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.261][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.262][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.285][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.286][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.288][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.311][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.312][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.314][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.330][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.334][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.338][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.342][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.343][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.344][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.345][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.356][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.358][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.359][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.364][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.365][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.367][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.371][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.372][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.374][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.379][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.381][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.385][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.386][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.388][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.392][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.393][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.394][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.398][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.400][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.401][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.405][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.406][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.408][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.412][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.413][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.415][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.419][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.420][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.422][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.429][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.433][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.434][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.436][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.440][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.441][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.443][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.447][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.448][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.450][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.454][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.457][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.465][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.466][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.468][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.472][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.473][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.475][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.479][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.482][ef$get] fields variable is a list.
biodb.INFO [2025-02-14 20:11:12.488][biodb::testThat]
biodb.INFO [2025-02-14 20:11:12.489][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-14 20:11:12.490][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:12.491][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:12.505][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-14 20:11:12.512][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-14 20:11:12.516][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:12.518][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-14 20:11:12.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-02-14 20:11:12.521][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-14 20:11:12.524][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-02-14 20:11:12.525][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-14 20:11:12.549][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:12.551][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:12.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:12.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:12.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:12.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:12.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:12.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:12.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:12.565][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.568][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.573][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.574][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.576][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.578][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.581][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.583][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.584][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.590][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.591][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.592][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.594][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.604][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.606][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.611][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.612][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.613][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.619][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.620][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.621][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.623][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.627][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.628][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.630][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.631][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.635][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.636][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.638][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.639][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.643][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.644][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.646][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.647][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.651][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.652][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.654][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.660][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.661][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.662][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.671][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.676][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.677][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.679][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.684][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.685][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.687][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.692][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.693][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.694][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.696][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.699][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.700][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.702][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.707][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:12.708][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.710][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.712][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:12.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.731][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.750][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:12.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:12.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.780][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.784][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:12.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:12.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.799][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.803][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:12.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.814][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:12.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:12.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:12.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:12.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.856][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.864][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:12.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:12.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.902][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:12.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.906][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.910][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:12.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:12.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.929][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:12.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.944][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:12.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:12.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:12.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:12.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.968][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:12.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:12.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.972][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:12.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.980][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:12.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:12.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:12.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:12.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:12.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:12.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:13.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:13.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:13.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:13.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.011][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-14 20:11:13.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-14 20:11:13.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-14 20:11:13.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-14 20:11:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-14 20:11:13.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-14 20:11:13.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-14 20:11:13.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-14 20:11:13.030][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.031][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-14 20:11:13.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:13.032][biodb::testThat]
biodb.TRACE[2025-02-14 20:11:13.036][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.037][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.039][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.040][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-02-14 20:11:13.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.079][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-02-14 20:11:13.080][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-02-14 20:11:13.081][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-14 20:11:13.082][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-14 20:11:13.084][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.085][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.087][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:13.088][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.089][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:13.090][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:13.091][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:13.092][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:13.093][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:13.094][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:13.095][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-14 20:11:13.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.112][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:13.113][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:13.114][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-02-14 20:11:13.125][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.126][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.128][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.130][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-02-14 20:11:13.145][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.149][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.153][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.159][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-02-14 20:11:13.211][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-14 20:11:13.212][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-02-14 20:11:13.213][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-02-14 20:11:13.227][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.228][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.229][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:13.231][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.232][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:13.246][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:13.248][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:13.249][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:13.250][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:13.255][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:13.256][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-14 20:11:13.258][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.262][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.265][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:13.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:13.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.273][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:13.274][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:13.275][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-02-14 20:11:13.286][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.287][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.289][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.290][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-02-14 20:11:13.301][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.305][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.309][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.316][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-02-14 20:11:13.317][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-02-14 20:11:13.318][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-02-14 20:11:13.319][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-02-14 20:11:13.321][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.322][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.323][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:13.325][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.326][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:13.327][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:13.328][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:13.329][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:13.330][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:13.331][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:13.332][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-14 20:11:13.334][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.338][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.342][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.350][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:13.351][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:13.352][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-02-14 20:11:13.366][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.367][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-02-14 20:11:13.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:13.369][biodb::testThat]
biodb.TRACE[2025-02-14 20:11:13.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.406][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-02-14 20:11:13.408][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-14 20:11:13.409][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-14 20:11:13.410][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.412][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.413][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:13.414][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:13.415][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:13.417][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:13.418][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:13.419][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:13.419][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:13.420][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:13.421][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-14 20:11:13.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:13.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:13.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:13.439][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:13.440][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-02-14 20:11:13.454][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.455][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-02-14 20:11:13.456][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:13.457][biodb::testThat]
biodb.TRACE[2025-02-14 20:11:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-14 20:11:13.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-14 20:11:13.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.489][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-14 20:11:13.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-14 20:11:13.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.540][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-14 20:11:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-14 20:11:13.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-14 20:11:13.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:13.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-14 20:11:13.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-14 20:11:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-14 20:11:13.561][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.562][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-14 20:11:13.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:13.564][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.571][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.572][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-14 20:11:13.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:13.574][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.582][biodb::testThat]
biodb.INFO [2025-02-14 20:11:13.583][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-14 20:11:13.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:13.585][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:13.588][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-02-14 20:11:19.368][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-02-14 20:11:19.454][biodb::testThat]
biodb.INFO [2025-02-14 20:11:19.457][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-14 20:11:19.459][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:19.460][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:19.684][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-02-14 20:11:19.725][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:19.727][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:19.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.732][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.734][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:19.737][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:19.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.741][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.743][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:19.746][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:19.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.750][ef$get] fields variable is a list.
biodb.INFO [2025-02-14 20:11:19.753][biodb::testThat]
biodb.INFO [2025-02-14 20:11:19.756][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-02-14 20:11:19.758][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:19.760][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:19.764][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-02-14 20:11:19.919][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-14 20:11:19.922][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:19.924][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-14 20:11:19.943][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-02-14 20:11:19.944][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-14 20:11:19.945][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-14 20:11:19.946][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-14 20:11:19.948][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:19.949][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:19.951][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:19.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:19.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:19.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:19.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:19.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:19.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:19.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:19.964][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:19.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.968][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:19.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:19.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:19.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:19.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:19.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:19.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:19.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:19.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:19.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:19.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:19.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:19.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:20.042][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-02-14 20:11:20.043][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-02-14 20:11:20.060][biodb::testThat]
biodb.INFO [2025-02-14 20:11:20.062][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-02-14 20:11:20.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:20.064][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:20.071][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-02-14 20:11:20.073][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-02-14 20:11:20.074][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-14 20:11:20.075][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.077][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-14 20:11:20.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-02-14 20:11:20.080][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-14 20:11:20.081][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-14 20:11:20.082][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-14 20:11:20.084][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.085][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:20.086][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:20.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:20.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.098][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.TRACE[2025-02-14 20:11:20.099][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:20.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:20.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.104][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:20.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:20.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:20.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:20.132][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-02-14 20:11:20.133][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-02-14 20:11:20.134][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-02-14 20:11:20.147][biodb::testThat]
biodb.INFO [2025-02-14 20:11:20.149][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-02-14 20:11:20.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:20.151][biodb::testThat]
biodb.INFO [2025-02-14 20:11:20.178][biodb::testThat]
biodb.INFO [2025-02-14 20:11:20.180][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-02-14 20:11:20.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:20.182][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:20.184][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.186][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.187][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:20.189][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.190][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:20.191][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:20.192][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:20.193][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:20.194][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-02-14 20:11:20.202][biodb::testThat]
biodb.INFO [2025-02-14 20:11:20.203][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-02-14 20:11:20.204][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:20.205][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:20.207][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.209][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.210][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:20.212][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:20.213][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:20.214][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:20.215][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:20.216][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:20.217][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-02-14 20:11:20.226][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:20.227][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:20.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.229][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.230][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:20.231][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:20.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.233][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:20.234][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:20.235][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:20.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:20.237][ef$get] fields variable is a list.
biodb.INFO [2025-02-14 20:11:20.238][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-14 20:11:20.239][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-14 20:11:20.248][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-14 20:11:20.249][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-14 20:11:20.250][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.252][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.253][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-14 20:11:20.258][biodb::testContext]
biodb.INFO [2025-02-14 20:11:20.259][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:20.260][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-02-14 20:11:20.261][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:20.262][biodb::testContext]
biodb.INFO [2025-02-14 20:11:20.267][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-14 20:11:20.268][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-14 20:11:20.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:20.273][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-14 20:11:20.279][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-14 20:11:20.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.284][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-14 20:11:20.285][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-14 20:11:20.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.288][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-14 20:11:20.289][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-14 20:11:20.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.293][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-14 20:11:20.294][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-14 20:11:20.295][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-14 20:11:20.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.299][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-14 20:11:20.300][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-14 20:11:20.301][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-14 20:11:20.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.304][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-14 20:11:20.305][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-14 20:11:20.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.309][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-14 20:11:20.310][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-14 20:11:20.311][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-14 20:11:20.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.315][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-14 20:11:20.316][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-14 20:11:20.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.320][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-14 20:11:20.321][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-14 20:11:20.322][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-14 20:11:20.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.325][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-14 20:11:20.326][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-14 20:11:20.327][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-14 20:11:20.328][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-14 20:11:20.329][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-14 20:11:20.331][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-14 20:11:20.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.334][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-14 20:11:20.335][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-14 20:11:20.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.339][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-14 20:11:20.340][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-14 20:11:20.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.344][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-14 20:11:20.345][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-14 20:11:20.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.349][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-14 20:11:20.350][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-14 20:11:20.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.353][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-14 20:11:20.354][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-14 20:11:20.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.358][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-14 20:11:20.359][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-14 20:11:20.362][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-14 20:11:20.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.366][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-14 20:11:20.367][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-14 20:11:20.368][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-14 20:11:20.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.372][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-14 20:11:20.374][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.375][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-14 20:11:20.376][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:20.378][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.379][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.380][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.382][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-14 20:11:20.383][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:20.384][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.385][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-14 20:11:20.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:20.388][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.393][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.394][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:20.394][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-14 20:11:20.394][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-14 20:11:20.394][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-14 20:11:20.394][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-14 20:11:20.396][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:20.397][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.399][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:20.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.402][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.403][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:20.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:20.405][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.406][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.408][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-14 20:11:20.409][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.410][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-14 20:11:20.411][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.412][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:20.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.415][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.417][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-14 20:11:20.418][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:20.419][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.421][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-14 20:11:20.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:20.423][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.424][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.425][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:20.425][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-14 20:11:20.425][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-14 20:11:20.425][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-14 20:11:20.425][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-14 20:11:20.426][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:20.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:20.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.433][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:20.434][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:20.435][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.437][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.438][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-14 20:11:20.440][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.441][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-14 20:11:20.442][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.443][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:20.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.448][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-14 20:11:20.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:20.450][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.451][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-14 20:11:20.452][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:20.453][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.454][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.455][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.456][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:20.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.459][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:20.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.463][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:20.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:20.466][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.467][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.468][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-14 20:11:20.470][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.471][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-14 20:11:20.472][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:20.474][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.475][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.476][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.477][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.478][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-14 20:11:20.479][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:20.480][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.481][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-14 20:11:20.482][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:20.483][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.484][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.485][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.486][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:20.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:20.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.493][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:20.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:20.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.497][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.498][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:20.499][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.514][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[2025-02-14 20:11:20.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.537][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[2025-02-14 20:11:20.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.564][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[2025-02-14 20:11:20.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.569][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[2025-02-14 20:11:20.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.592][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[2025-02-14 20:11:20.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.602][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-14 20:11:20.606][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-14 20:11:20.608][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-14 20:11:20.610][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-14 20:11:20.612][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-14 20:11:20.615][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-14 20:11:20.617][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-14 20:11:20.619][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-14 20:11:20.622][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-14 20:11:20.624][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-14 20:11:20.627][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-14 20:11:20.629][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-14 20:11:20.631][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-14 20:11:20.633][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-14 20:11:20.635][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-14 20:11:20.637][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-14 20:11:20.639][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-14 20:11:20.641][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-14 20:11:20.643][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-14 20:11:20.645][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-14 20:11:20.699][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-14 20:11:20.704][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-14 20:11:20.708][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-14 20:11:20.710][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-14 20:11:20.713][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-14 20:11:20.716][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-14 20:11:20.718][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-14 20:11:20.720][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-14 20:11:20.722][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-14 20:11:20.724][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-14 20:11:20.726][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-14 20:11:20.728][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-14 20:11:20.730][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-14 20:11:20.732][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-14 20:11:20.734][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-14 20:11:20.736][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-14 20:11:20.738][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-14 20:11:20.740][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-14 20:11:20.742][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-14 20:11:20.745][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-14 20:11:20.748][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-14 20:11:20.750][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-14 20:11:20.752][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-14 20:11:20.753][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-14 20:11:20.755][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-14 20:11:20.757][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-14 20:11:20.759][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-14 20:11:20.761][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-14 20:11:20.763][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-14 20:11:20.764][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-14 20:11:20.766][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-14 20:11:20.768][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-14 20:11:20.770][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-14 20:11:20.772][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-14 20:11:20.774][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-14 20:11:20.776][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-14 20:11:20.778][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-14 20:11:20.780][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-14 20:11:20.781][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-14 20:11:20.783][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-14 20:11:20.785][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-14 20:11:20.787][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-14 20:11:20.788][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-14 20:11:20.790][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-14 20:11:20.792][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-14 20:11:20.794][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-14 20:11:20.796][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-14 20:11:20.798][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-14 20:11:20.799][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-14 20:11:20.801][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-14 20:11:20.802][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-14 20:11:20.803][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-14 20:11:20.805][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-14 20:11:20.806][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-14 20:11:20.808][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-14 20:11:20.809][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-14 20:11:20.811][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-14 20:11:20.812][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-14 20:11:20.813][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-14 20:11:20.815][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-14 20:11:20.816][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-14 20:11:20.818][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-14 20:11:20.819][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-14 20:11:20.821][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-14 20:11:20.823][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-14 20:11:20.824][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:20.825][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.826][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:20.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:20.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:20.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:20.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:20.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:20.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:20.938][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[2025-02-14 20:11:20.940][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-14 20:11:20.942][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:20.948][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.950][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.952][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:20.953][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.954][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-14 20:11:20.955][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.957][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-14 20:11:20.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:20.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.959][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-14 20:11:20.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-14 20:11:20.961][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-14 20:11:20.963][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:20.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:20.964][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-14 20:11:20.964][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-14 20:11:20.965][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-14 20:11:20.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:20.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:20.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:20.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:20.971][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-14 20:11:20.971][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-14 20:11:20.972][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:20.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:20.974][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:20.975][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:20.976][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-14 20:11:20.978][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-14 20:11:20.979][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-14 20:11:20.981][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-14 20:11:20.982][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-14 20:11:20.986][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:20.987][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-14 20:11:20.988][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:20.990][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:20.991][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:20.992][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:20.993][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-14 20:11:20.994][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-02-14 20:11:20.995][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-14 20:11:20.995][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-02-14 20:11:20.996][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:20.997][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:20.998][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-02-14 20:11:20.999][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-02-14 20:11:21.000][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:21.001][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:21.002][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:21.003][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:21.005][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:21.006][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:21.007][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-02-14 20:11:21.008][biodb::testThat]
biodb.INFO [2025-02-14 20:11:21.009][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-02-14 20:11:21.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:21.011][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:21.016][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:21.017][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:21.018][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:21.020][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:21.021][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:21.022][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:21.023][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:21.024][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:21.025][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:21.029][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-02-14 20:11:21.034][biodb::testThat]
biodb.INFO [2025-02-14 20:11:21.035][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-02-14 20:11:21.036][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:21.037][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:21.039][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-02-14 20:11:21.040][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-14 20:11:21.042][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:21.043][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-14 20:11:21.045][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-02-14 20:11:21.046][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-14 20:11:21.048][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-02-14 20:11:21.049][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-14 20:11:21.051][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:21.052][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:21.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:21.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:21.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:21.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:21.072][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.073][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.075][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.080][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.081][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.083][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.084][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.088][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.089][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.091][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.092][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.096][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.097][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.099][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.100][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.107][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.112][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.113][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.115][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.123][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.125][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.129][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.130][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.131][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.133][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.137][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.138][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.140][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.142][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.146][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.147][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.149][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.154][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:21.155][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:21.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.157][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.159][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:21.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:21.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.163][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:21.164][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:21.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.166][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:21.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:21.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.172][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.177][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.179][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.188][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.193][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.194][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.196][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.201][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:21.202][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:21.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.204][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.205][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:21.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:21.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.209][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:21.210][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:21.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.212][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:21.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:21.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.217][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:21.218][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.220][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.221][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:21.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.237][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.241][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.244][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:21.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.248][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.252][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.256][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:21.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:21.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:21.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.295][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:21.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.302][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.318][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:21.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:21.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.325][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:21.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:21.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.329][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:21.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:21.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:21.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:21.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:21.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:21.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:21.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:21.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:21.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:21.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:21.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:21.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:21.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.368][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.375][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:21.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:21.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.410][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.414][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:21.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.418][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.422][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.426][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:21.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.430][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:21.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:21.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.434][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:21.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:21.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.437][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:21.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:21.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:21.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.457][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:21.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:21.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:21.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:21.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.481][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:21.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:21.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.485][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:21.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:21.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.498][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:21.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:21.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:21.525][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-02-14 20:11:21.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:21.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:21.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:21.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:21.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-14 20:11:21.543][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-14 20:11:21.544][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-14 20:11:21.545][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-14 20:11:21.546][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-14 20:11:21.547][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:21.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:21.548][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.550][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-14 20:11:21.555][biodb::testContext]
biodb.INFO [2025-02-14 20:11:21.556][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:21.557][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-02-14 20:11:21.558][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-14 20:11:21.559][biodb::testContext]
biodb.INFO [2025-02-14 20:11:21.563][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-14 20:11:21.564][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-14 20:11:21.568][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:21.569][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-14 20:11:21.570][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-14 20:11:21.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.574][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-14 20:11:21.575][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-14 20:11:21.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.578][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-14 20:11:21.579][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-14 20:11:21.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.583][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-14 20:11:21.584][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-14 20:11:21.585][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-14 20:11:21.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.589][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-14 20:11:21.590][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-14 20:11:21.591][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-14 20:11:21.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.594][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-14 20:11:21.595][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-14 20:11:21.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.604][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-14 20:11:21.606][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-14 20:11:21.607][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-14 20:11:21.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.610][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-14 20:11:21.611][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-14 20:11:21.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.615][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-14 20:11:21.616][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-14 20:11:21.617][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-14 20:11:21.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.621][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-14 20:11:21.622][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-14 20:11:21.623][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-14 20:11:21.624][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-14 20:11:21.624][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-14 20:11:21.626][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-14 20:11:21.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.629][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-14 20:11:21.630][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-14 20:11:21.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.634][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-14 20:11:21.635][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-14 20:11:21.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.638][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-14 20:11:21.639][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-14 20:11:21.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.643][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-14 20:11:21.644][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-14 20:11:21.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.648][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-14 20:11:21.649][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-14 20:11:21.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.651][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[2025-02-14 20:11:21.652][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-14 20:11:21.653][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-14 20:11:21.657][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-14 20:11:21.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.661][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-14 20:11:21.662][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-14 20:11:21.663][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-14 20:11:21.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.667][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-14 20:11:21.668][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.669][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-14 20:11:21.670][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.671][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:21.672][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.673][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.674][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.676][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-14 20:11:21.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:21.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.679][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-14 20:11:21.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:21.681][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.683][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:21.683][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-14 20:11:21.683][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-14 20:11:21.683][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-14 20:11:21.683][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-14 20:11:21.684][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:21.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.687][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:21.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.691][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:21.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:21.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.695][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.696][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-14 20:11:21.698][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.699][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-14 20:11:21.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:21.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.706][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-14 20:11:21.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:21.713][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.714][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-14 20:11:21.715][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:21.716][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.717][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.718][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:21.718][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-14 20:11:21.718][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-14 20:11:21.718][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-14 20:11:21.718][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-14 20:11:21.719][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:21.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.722][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:21.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.724][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.725][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.726][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:21.727][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:21.728][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.729][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.730][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-14 20:11:21.732][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.733][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-14 20:11:21.734][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.735][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:21.736][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.739][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.740][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-14 20:11:21.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:21.742][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.743][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-14 20:11:21.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:21.745][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.746][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.747][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.748][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:21.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.750][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:21.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.754][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.755][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:21.756][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:21.757][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.758][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.759][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-14 20:11:21.761][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.762][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-14 20:11:21.763][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.764][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:21.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.768][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-14 20:11:21.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:21.770][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.771][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-14 20:11:21.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:21.773][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.774][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:21.775][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.776][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-14 20:11:21.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:21.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:21.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:21.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:21.783][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.784][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:21.785][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:21.785][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:21.786][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:21.788][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:21.789][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:21.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:21.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:21.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:21.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:21.872][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-14 20:11:21.874][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-14 20:11:21.875][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-14 20:11:21.877][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-14 20:11:21.878][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-14 20:11:21.880][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-14 20:11:21.881][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-14 20:11:21.882][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-14 20:11:21.884][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-14 20:11:21.885][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-14 20:11:21.887][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-14 20:11:21.888][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-14 20:11:21.889][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-14 20:11:21.891][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-14 20:11:21.892][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-14 20:11:21.894][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-14 20:11:21.895][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-14 20:11:21.896][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-14 20:11:21.898][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-14 20:11:21.899][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-14 20:11:21.901][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-14 20:11:21.902][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-14 20:11:21.904][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-14 20:11:21.905][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-14 20:11:21.906][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-14 20:11:21.908][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-14 20:11:21.909][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-14 20:11:21.911][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-14 20:11:21.912][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-14 20:11:21.913][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-14 20:11:21.915][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-14 20:11:21.916][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-14 20:11:21.923][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-14 20:11:21.925][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-14 20:11:21.926][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-14 20:11:21.928][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-14 20:11:21.929][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-14 20:11:21.930][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-14 20:11:21.932][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-14 20:11:21.933][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-14 20:11:21.934][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-14 20:11:21.936][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-14 20:11:21.937][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-14 20:11:21.939][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-14 20:11:21.940][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-14 20:11:21.942][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-14 20:11:21.943][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-14 20:11:21.944][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-14 20:11:21.946][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-14 20:11:21.947][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-14 20:11:21.949][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-14 20:11:21.950][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-14 20:11:21.952][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-14 20:11:21.953][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-14 20:11:21.955][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-14 20:11:21.956][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-14 20:11:21.957][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-14 20:11:21.959][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-14 20:11:21.960][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-14 20:11:21.962][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-14 20:11:21.963][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-14 20:11:21.964][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-14 20:11:21.966][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-14 20:11:21.967][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-14 20:11:21.969][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-14 20:11:21.970][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-14 20:11:21.972][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-14 20:11:21.973][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-14 20:11:21.974][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-14 20:11:21.976][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-14 20:11:21.977][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-14 20:11:21.979][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-14 20:11:21.980][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-14 20:11:21.981][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-14 20:11:21.983][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-14 20:11:21.984][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-14 20:11:21.986][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-14 20:11:21.987][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-14 20:11:21.988][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-14 20:11:21.990][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-14 20:11:21.991][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-14 20:11:21.992][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-14 20:11:21.994][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-14 20:11:21.995][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-14 20:11:21.997][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-14 20:11:21.998][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-14 20:11:21.999][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.001][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.031][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[2025-02-14 20:11:22.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.074][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[2025-02-14 20:11:22.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.098][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[2025-02-14 20:11:22.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-14 20:11:22.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.112][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-14 20:11:22.113][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:22.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:22.116][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-14 20:11:22.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:22.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-14 20:11:22.119][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:22.120][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-14 20:11:22.121][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:22.122][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-14 20:11:22.123][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-14 20:11:22.130][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-14 20:11:22.131][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:22.132][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-14 20:11:22.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-14 20:11:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-14 20:11:22.135][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-14 20:11:22.136][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-14 20:11:22.136][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-14 20:11:22.136][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-14 20:11:22.137][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-14 20:11:22.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:22.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:22.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-14 20:11:22.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-14 20:11:22.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-14 20:11:22.143][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-14 20:11:22.144][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-14 20:11:22.144][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-14 20:11:22.145][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:22.145][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:22.146][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-14 20:11:22.147][self$setPropertyValue]
biodb.DEBUG[2025-02-14 20:11:22.148][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-14 20:11:22.150][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-14 20:11:22.151][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-14 20:11:22.153][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-14 20:11:22.154][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-14 20:11:22.158][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:22.158][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-14 20:11:22.160][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:22.161][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:22.162][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:22.163][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:22.164][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-14 20:11:22.165][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-02-14 20:11:22.166][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-14 20:11:22.166][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-02-14 20:11:22.167][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-14 20:11:22.168][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-14 20:11:22.169][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-02-14 20:11:22.170][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-02-14 20:11:22.171][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-14 20:11:22.173][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:22.174][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:22.175][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:22.176][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-14 20:11:22.177][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-14 20:11:22.178][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-02-14 20:11:22.180][biodb::testThat]
biodb.INFO [2025-02-14 20:11:22.181][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2025-02-14 20:11:22.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-14 20:11:22.182][biodb::testThat]
biodb.DEBUG[2025-02-14 20:11:22.185][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-14 20:11:22.186][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-02-14 20:11:22.187][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-02-14 20:11:22.190][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:22.191][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:22.193][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:22.194][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:22.195][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:22.196][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:22.197][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:22.198][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:22.199][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:22.200][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:22.201][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-02-14 20:11:22.203][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-14 20:11:22.204][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-14 20:11:22.205][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:22.207][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-14 20:11:22.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-02-14 20:11:22.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-14 20:11:22.212][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-02-14 20:11:22.213][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-14 20:11:22.214][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:22.215][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:22.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:22.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:22.230][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.231][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.233][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.243][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.245][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.246][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.248][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.252][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.253][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.255][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.256][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.260][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.261][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.263][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.264][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.268][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.271][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.276][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.277][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.279][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.285][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.286][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.287][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.289][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.293][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.294][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.296][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.301][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.302][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.304][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.309][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.310][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.312][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.318][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.319][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.321][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.326][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.327][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.329][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.334][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.335][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.337][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.351][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.357][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.358][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.360][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.365][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.366][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.368][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.373][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.375][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.376][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.378][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.382][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:22.383][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.385][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.386][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:22.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.403][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.407][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.411][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.419][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.423][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.478][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.502][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.506][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.510][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.514][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.549][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.553][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.557][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.593][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.601][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.605][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.609][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.620][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.624][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:22.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.640][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:22.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.664][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:22.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:22.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.667][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:22.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:22.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.680][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:22.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:22.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:22.707][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-14 20:11:22.708][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.717][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.722][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:22.731][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:22.732][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:22.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:22.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:22.746][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-02-14 20:11:22.747][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-14 20:11:22.749][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:22.751][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-14 20:11:22.753][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-02-14 20:11:22.754][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-14 20:11:22.756][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-02-14 20:11:22.757][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-14 20:11:22.759][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-14 20:11:22.760][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-14 20:11:22.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:22.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:22.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:22.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:22.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:22.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:22.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:22.777][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.779][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.781][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.787][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.788][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.790][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.791][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:22.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.796][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.797][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.799][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.800][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.818][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.820][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.822][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.824][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.829][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.831][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.837][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.838][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.840][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.845][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.847][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.849][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.850][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:22.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.854][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.855][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.857][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.858][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.862][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.863][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.865][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:22.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.870][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.871][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.873][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:22.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.878][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.879][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:22.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:22.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.889][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:22.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:22.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.898][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:22.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.903][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.904][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.906][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:22.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.911][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.912][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.914][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:22.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:22.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.920][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.921][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.927][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.929][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:22.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:22.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.933][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.934][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.936][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.938][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:22.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.941][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:22.942][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.944][ef$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.946][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-14 20:11:22.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:22.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:22.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:22.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.961][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.969][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-14 20:11:22.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.973][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.977][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.981][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-14 20:11:22.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-14 20:11:22.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:22.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:22.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:22.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:23.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:23.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:23.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-14 20:11:23.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:23.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.012][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:23.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:23.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:23.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-14 20:11:23.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:23.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:23.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.028][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:23.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-14 20:11:23.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.038][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:23.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:23.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:23.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:23.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.047][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:23.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-14 20:11:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.055][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.058][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:23.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:23.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:23.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:23.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-14 20:11:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-14 20:11:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:23.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:23.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:23.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:23.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-14 20:11:23.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-14 20:11:23.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.098][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:23.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:23.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.102][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:23.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.105][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:23.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-14 20:11:23.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:23.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:23.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:23.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:23.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:23.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-14 20:11:23.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.133][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:23.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:23.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.137][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:23.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:23.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:23.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-14 20:11:23.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.151][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:23.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:23.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:23.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:23.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.159][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:23.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-14 20:11:23.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:23.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:23.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:23.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:23.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.171][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-14 20:11:23.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-14 20:11:23.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.175][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:23.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.190][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-14 20:11:23.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-14 20:11:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-14 20:11:23.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-14 20:11:23.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.215][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:23.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:23.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.219][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:23.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:23.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.227][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:23.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-14 20:11:23.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-14 20:11:23.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-14 20:11:23.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:23.260][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-02-14 20:11:23.261][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.265][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.272][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:23.276][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:23.277][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:23.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:23.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:23.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:23.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:23.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:23.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:23.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:23.293][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-14 20:11:23.294][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-02-14 20:11:23.295][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-02-14 20:11:23.297][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:23.298][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:23.300][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:23.301][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:23.302][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:23.303][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:23.304][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:23.305][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:23.306][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:23.307][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:23.308][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-14 20:11:23.310][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.314][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.318][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.322][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.325][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.329][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.333][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:23.337][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:23.338][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:23.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:23.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:23.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:23.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:23.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:23.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:23.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:23.349][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.353][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.362][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.366][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.370][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.374][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.378][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:23.382][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-02-14 20:11:23.383][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:23.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:23.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:23.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:23.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:23.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:23.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:23.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-14 20:11:23.398][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-14 20:11:23.399][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-02-14 20:11:23.400][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-02-14 20:11:23.401][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:23.403][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:23.404][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-14 20:11:23.405][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-14 20:11:23.406][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-14 20:11:23.408][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-14 20:11:23.409][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-14 20:11:23.410][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-14 20:11:23.411][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-14 20:11:23.412][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-14 20:11:23.413][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-14 20:11:23.414][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.418][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.422][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.426][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.430][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.434][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:23.442][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-02-14 20:11:23.442][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-02-14 20:11:23.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:23.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:23.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:23.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:23.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:23.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:23.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-14 20:11:23.453][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.457][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.461][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.470][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.479][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-14 20:11:23.483][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-14 20:11:23.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-14 20:11:23.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-14 20:11:23.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-14 20:11:23.486][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-14 20:11:23.487][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-14 20:11:23.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-14 20:11:23.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:23.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:23.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:23.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:23.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:23.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-14 20:11:23.504][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-14 20:11:23.505][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-14 20:11:23.507][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-14 20:11:23.507][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-14 20:11:23.508][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-14 20:11:23.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-14 20:11:23.510][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-14 20:11:23.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-14 20:11:23.512][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-14 20:11:23.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
>
> proc.time()
user system elapsed
8.609 0.698 15.111