Pierrick Roger
| Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-14 11:39 -0400 (Fri, 14 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
| 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 204/2309 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbHmdb |
| Version: 1.13.0 |
| 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: 2025-03-13 20:13:40 -0400 (Thu, 13 Mar 2025) |
| EndedAt: 2025-03-13 20:14:50 -0400 (Thu, 13 Mar 2025) |
| EllapsedTime: 70.1 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) (2025-02-19 r87757)
* 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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) (2025-02-19 r87757) -- "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.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-03-13 20:14:12.206][biodb::testContext]
biodb.INFO [2025-03-13 20:14:12.208][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:12.209][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-03-13 20:14:12.210][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:12.211][biodb::testContext]
biodb.INFO [2025-03-13 20:14:12.213][biodb::testThat]
biodb.INFO [2025-03-13 20:14:12.214][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2025-03-13 20:14:12.215][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:12.216][biodb::testThat]
biodb.INFO [2025-03-13 20:14:12.338][biodb::testContext]
biodb.INFO [2025-03-13 20:14:12.340][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:12.341][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-13 20:14:12.342][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:12.343][biodb::testContext]
biodb.INFO [2025-03-13 20:14:12.352][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-13 20:14:12.355][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 20:14:12.362][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:12.363][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 20:14:12.364][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 20:14:12.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.368][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 20:14:12.407][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 20:14:12.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.412][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 20:14:12.413][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 20:14:12.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.417][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 20:14:12.418][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 20:14:12.419][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 20:14:12.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.423][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 20:14:12.424][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 20:14:12.425][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 20:14:12.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.429][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 20:14:12.431][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 20:14:12.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.435][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 20:14:12.436][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 20:14:12.437][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 20:14:12.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.441][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 20:14:12.442][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 20:14:12.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 20:14:12.447][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 20:14:12.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 20:14:12.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.452][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 20:14:12.453][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 20:14:12.454][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 20:14:12.455][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 20:14:12.456][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 20:14:12.457][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 20:14:12.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.461][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 20:14:12.462][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 20:14:12.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.466][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 20:14:12.467][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 20:14:12.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.471][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 20:14:12.472][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 20:14:12.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.475][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 20:14:12.477][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 20:14:12.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.480][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 20:14:12.481][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 20:14:12.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.485][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 20:14:12.486][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 20:14:12.489][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 20:14:12.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.493][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 20:14:12.494][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 20:14:12.495][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 20:14:12.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.501][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 20:14:12.535][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.551][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-13 20:14:12.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.553][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:12.554][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.556][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.557][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.558][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 20:14:12.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:12.560][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.561][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 20:14:12.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:12.563][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.564][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.565][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:12.565][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 20:14:12.565][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 20:14:12.565][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 20:14:12.565][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 20:14:12.566][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:12.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.569][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:12.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.577][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.578][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.579][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:12.580][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:12.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.582][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.583][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 20:14:12.585][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.586][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 20:14:12.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.587][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:12.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.590][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.592][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 20:14:12.593][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:12.594][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.595][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 20:14:12.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:12.597][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.599][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:12.599][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 20:14:12.599][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 20:14:12.599][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 20:14:12.599][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 20:14:12.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:12.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.602][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:12.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.605][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.606][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.607][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:12.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:12.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.610][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.611][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 20:14:12.612][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.613][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-13 20:14:12.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:12.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.619][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.620][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 20:14:12.621][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:12.622][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.623][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 20:14:12.624][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:12.625][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.626][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.627][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.628][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:12.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:12.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.634][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.635][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:12.636][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:12.637][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.637][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.639][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 20:14:12.640][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.641][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 20:14:12.642][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.643][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:12.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.645][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.646][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.647][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.648][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 20:14:12.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:12.650][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.651][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 20:14:12.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:12.653][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:12.655][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.656][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:12.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:12.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:12.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:12.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:12.662][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:12.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:12.665][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:12.666][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:12.669][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:12.670][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.732][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[2025-03-13 20:14:12.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.736][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[2025-03-13 20:14:12.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.740][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[2025-03-13 20:14:12.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.745][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[2025-03-13 20:14:12.750][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 20:14:12.754][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 20:14:12.756][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 20:14:12.757][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 20:14:12.758][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 20:14:12.760][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 20:14:12.761][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 20:14:12.762][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 20:14:12.764][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 20:14:12.765][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 20:14:12.766][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 20:14:12.767][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 20:14:12.769][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 20:14:12.770][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 20:14:12.771][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 20:14:12.773][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 20:14:12.774][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 20:14:12.775][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 20:14:12.777][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 20:14:12.778][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 20:14:12.779][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 20:14:12.780][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 20:14:12.782][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 20:14:12.783][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 20:14:12.784][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 20:14:12.786][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 20:14:12.787][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 20:14:12.788][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 20:14:12.790][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 20:14:12.791][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 20:14:12.792][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 20:14:12.794][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 20:14:12.795][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 20:14:12.796][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 20:14:12.798][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 20:14:12.799][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 20:14:12.800][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 20:14:12.802][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 20:14:12.803][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 20:14:12.804][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 20:14:12.806][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 20:14:12.807][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 20:14:12.808][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 20:14:12.810][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 20:14:12.811][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 20:14:12.812][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 20:14:12.814][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 20:14:12.815][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 20:14:12.816][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 20:14:12.818][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 20:14:12.819][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 20:14:12.820][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 20:14:12.822][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 20:14:12.823][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 20:14:12.824][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 20:14:12.826][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 20:14:12.827][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 20:14:12.828][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 20:14:12.830][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 20:14:12.831][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 20:14:12.832][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 20:14:12.834][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 20:14:12.835][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 20:14:12.836][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 20:14:12.838][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 20:14:12.839][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 20:14:12.840][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 20:14:12.841][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 20:14:12.843][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 20:14:12.844][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 20:14:12.845][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 20:14:12.847][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 20:14:12.848][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 20:14:12.849][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 20:14:12.851][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 20:14:12.852][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 20:14:12.853][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 20:14:12.855][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 20:14:12.856][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 20:14:12.857][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 20:14:12.859][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 20:14:12.860][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 20:14:12.861][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 20:14:12.867][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 20:14:12.869][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-13 20:14:12.872][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:12.873][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.875][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:12.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:12.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:12.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:12.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:12.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:12.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:12.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:13.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:13.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:13.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:13.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:13.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:13.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:13.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:13.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:13.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:13.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:13.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:13.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:13.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:13.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:13.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:13.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:13.015][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-13 20:14:13.026][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:13.028][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:13.029][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 20:14:13.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:13.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:13.032][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:13.033][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-13 20:14:13.034][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:13.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:13.036][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 20:14:13.037][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:13.038][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:13.039][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-13 20:14:13.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-13 20:14:13.041][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-13 20:14:13.043][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:13.044][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:13.044][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-13 20:14:13.044][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-13 20:14:13.045][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 20:14:13.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:13.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:13.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:13.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:13.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:13.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:13.051][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-13 20:14:13.051][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-13 20:14:13.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:13.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:13.054][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:13.055][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:13.061][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-13 20:14:13.063][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 20:14:13.064][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 20:14:13.066][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 20:14:13.067][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 20:14:13.091][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:13.092][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-13 20:14:13.096][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:13.100][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:13.104][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:13.105][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:13.107][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-13 20:14:13.108][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-13 20:14:13.109][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-13 20:14:13.109][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-13 20:14:13.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:13.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:13.112][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-13 20:14:13.113][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-13 20:14:13.114][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:13.139][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:13.140][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:13.141][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:13.143][private$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[2025-03-13 20:14:13.144][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:13.145][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-13 20:14:13.153][biodb::testThat]
biodb.INFO [2025-03-13 20:14:13.154][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-13 20:14:13.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:13.156][biodb::testThat]
biodb.TRACE[2025-03-13 20:14:13.160][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[2025-03-13 20:14:13.162][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:13.165][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:13.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:13.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:13.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:13.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:13.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:13.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:13.182][FUN] Functions in observer BiodbConfig: [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[2025-03-13 20:14:13.194][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.195][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.215][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.216][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.218][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.244][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.249][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.250][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.252][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.254][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.259][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.260][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.264][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.268][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.276][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.277][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.284][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.285][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.288][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.300][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.301][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.304][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.308][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.309][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.310][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.316][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.317][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.324][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:13.325][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:13.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:13.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:13.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.332][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:13.333][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:13.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:13.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:13.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.340][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.341][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.349][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.350][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.357][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.366][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:13.367][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:13.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.370][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.374][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:13.375][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:13.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.379][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:13.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:13.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.383][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:13.384][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.386][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.387][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:13.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.440][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.449][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:13.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.452][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.456][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:13.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:13.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:13.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:13.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.522][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:13.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.526][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:13.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:13.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:13.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:13.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:13.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:13.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:13.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.568][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.572][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.576][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.609][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.621][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.633][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:13.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:13.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.637][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:13.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:13.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:13.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.645][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:13.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:13.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:13.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:13.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:13.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.704][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.708][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:13.748][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-13 20:14:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 20:14:13.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 20:14:13.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 20:14:13.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 20:14:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.759][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-13 20:14:13.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-13 20:14:13.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-13 20:14:13.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-13 20:14:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.826][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.834][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:13.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.859][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.860][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.862][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:13.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.876][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.880][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.893][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.894][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.897][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:13.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.921][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.922][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:13.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.937][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.941][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.945][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.949][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.950][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.952][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:13.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.977][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.996][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:13.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.003][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.004][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.007][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.034][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.048][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.052][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.056][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.060][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.061][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.082][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.086][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.100][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.104][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.108][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.112][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.113][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.139][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.141][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.152][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.156][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.164][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.165][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.171][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.195][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.196][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.198][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.199][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.210][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.214][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.222][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.223][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.238][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.242][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.246][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.250][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.251][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.254][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.276][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.277][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.280][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.303][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.304][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.322][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.326][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.330][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.334][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.335][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.337][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.348][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.349][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.356][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.357][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.363][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.364][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.371][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.372][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.373][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.378][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.379][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.385][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.386][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.392][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.393][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.395][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.399][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.400][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.406][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.407][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.413][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.414][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.420][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.421][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.428][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.429][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.443][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.444][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.448][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.454][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.460][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.461][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.467][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.468][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.473][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.474][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.476][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 20:14:14.483][biodb::testThat]
biodb.INFO [2025-03-13 20:14:14.484][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-13 20:14:14.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:14.486][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:14.499][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-13 20:14:14.506][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-13 20:14:14.510][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:14.512][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-13 20:14:14.514][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-13 20:14:14.515][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 20:14:14.517][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-13 20:14:14.518][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 20:14:14.542][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:14.544][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:14.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:14.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:14.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:14.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:14.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:14.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:14.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 20:14:14.558][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.559][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.566][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.567][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.570][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.574][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.575][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.577][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.578][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.582][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.583][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.586][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.597][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.604][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.605][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.607][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.612][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.613][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.616][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.620][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.621][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.629][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.630][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.632][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.633][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.638][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.639][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.646][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.647][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.654][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.663][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.671][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.672][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.674][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.679][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.680][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.682][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.687][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.689][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.692][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.698][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.700][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.704][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:14.705][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.707][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.708][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:14.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.724][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.727][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.737][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:14.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.741][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.745][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.749][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:14.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:14.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:14.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.810][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:14.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.814][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.822][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:14.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:14.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:14.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:14.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.863][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.866][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.871][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:14.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.907][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.911][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:14.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.915][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.919][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:14.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:14.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:14.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.938][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:14.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.954][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:14.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:14.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:14.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.982][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:14.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:14.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.990][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:14.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:14.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:14.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:14.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:14.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:15.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:15.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:15.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:15.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:15.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:15.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:15.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:15.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:15.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.022][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-13 20:14:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-13 20:14:15.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-13 20:14:15.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-13 20:14:15.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-13 20:14:15.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-13 20:14:15.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-13 20:14:15.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 20:14:15.042][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.043][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-13 20:14:15.044][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:15.045][biodb::testThat]
biodb.TRACE[2025-03-13 20:14:15.048][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.049][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.051][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.053][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-03-13 20:14:15.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.093][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-03-13 20:14:15.095][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-13 20:14:15.096][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-13 20:14:15.097][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-13 20:14:15.098][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.100][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.101][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:15.102][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.103][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:15.105][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:15.106][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:15.107][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:15.108][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:15.109][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:15.110][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-13 20:14:15.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.127][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:15.128][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:15.129][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-13 20:14:15.139][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.141][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.143][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.144][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-03-13 20:14:15.161][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.165][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.175][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[2025-03-13 20:14:15.228][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-13 20:14:15.230][private$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[2025-03-13 20:14:15.231][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-13 20:14:15.245][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.247][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.249][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:15.250][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.251][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:15.272][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:15.273][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:15.274][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:15.275][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:15.276][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:15.277][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-13 20:14:15.279][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.283][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.286][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.290][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:15.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:15.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.294][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:15.295][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:15.296][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-13 20:14:15.307][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.308][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.310][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.311][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-03-13 20:14:15.321][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.325][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.329][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.336][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-03-13 20:14:15.337][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-03-13 20:14:15.338][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-13 20:14:15.339][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-13 20:14:15.341][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.342][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.343][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:15.345][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.346][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:15.347][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:15.348][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:15.349][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:15.350][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:15.351][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:15.352][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-13 20:14:15.354][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.358][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.362][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.366][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:15.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.370][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:15.371][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:15.371][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-03-13 20:14:15.386][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.388][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-13 20:14:15.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:15.390][biodb::testThat]
biodb.TRACE[2025-03-13 20:14:15.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.428][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-13 20:14:15.429][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-13 20:14:15.430][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-13 20:14:15.432][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.433][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.435][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:15.436][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:15.437][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:15.438][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:15.439][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:15.440][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:15.441][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:15.442][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:15.443][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-13 20:14:15.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:15.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:15.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:15.463][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:15.464][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-03-13 20:14:15.479][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.480][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-13 20:14:15.481][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:15.482][biodb::testThat]
biodb.TRACE[2025-03-13 20:14:15.503][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.507][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-13 20:14:15.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-13 20:14:15.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-13 20:14:15.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-13 20:14:15.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 20:14:15.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-13 20:14:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-13 20:14:15.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:15.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-13 20:14:15.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-13 20:14:15.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:15.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 20:14:15.589][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.590][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-13 20:14:15.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:15.592][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.600][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.601][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-13 20:14:15.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:15.603][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.610][biodb::testThat]
biodb.INFO [2025-03-13 20:14:15.611][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-13 20:14:15.612][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:15.613][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:15.616][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-03-13 20:14:35.163][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-03-13 20:14:35.211][biodb::testThat]
biodb.INFO [2025-03-13 20:14:35.212][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-13 20:14:35.213][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:35.214][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:39.908][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-03-13 20:14:39.958][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:39.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:39.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:39.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:39.969][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:39.972][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:39.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:39.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:39.979][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:39.982][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:39.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:39.986][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 20:14:39.988][biodb::testThat]
biodb.INFO [2025-03-13 20:14:39.989][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-13 20:14:39.990][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:39.991][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:39.993][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-13 20:14:40.061][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-03-13 20:14:40.063][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-03-13 20:14:40.064][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-03-13 20:14:40.066][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-03-13 20:14:40.067][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-03-13 20:14:40.068][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-03-13 20:14:40.069][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-13 20:14:40.071][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-13 20:14:40.073][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-13 20:14:40.074][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-03-13 20:14:40.075][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker1d1d482657fb28marker".
biodb.TRACE[2025-03-13 20:14:40.077][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-03-13 20:14:40.078][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-13 20:14:40.079][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-13 20:14:40.080][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-03-13 20:14:40.081][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2025-03-13 20:14:40.082][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-13 20:14:40.083][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2025-03-13 20:14:40.090][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2025-03-13 20:14:40.091][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-03-13 20:14:40.092][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-03-13 20:14:40.094][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2025-03-13 20:14:40.102][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2025-03-13 20:14:40.103][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-13 20:14:40.104][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-13 20:14:40.105][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-03-13 20:14:40.107][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker1d1d48c189545marker".
biodb.TRACE[2025-03-13 20:14:40.108][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-03-13 20:14:40.109][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-03-13 20:14:40.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-13 20:14:40.126][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 20:14:40.128][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 20:14:40.129][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 20:14:40.130][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.131][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:40.132][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:40.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:40.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.177][FUN] Functions in observer BiodbConfig: [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[2025-03-13 20:14:40.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:40.210][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-13 20:14:40.211][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-13 20:14:40.226][biodb::testThat]
biodb.INFO [2025-03-13 20:14:40.227][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-13 20:14:40.228][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:40.229][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:40.236][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-03-13 20:14:40.238][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-03-13 20:14:40.239][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-13 20:14:40.240][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.242][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-13 20:14:40.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-03-13 20:14:40.245][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 20:14:40.246][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 20:14:40.247][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 20:14:40.248][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.249][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:40.250][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:40.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:40.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 20:14:40.263][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.267][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:40.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:40.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:40.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:40.299][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-13 20:14:40.300][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-13 20:14:40.301][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-03-13 20:14:40.313][biodb::testThat]
biodb.INFO [2025-03-13 20:14:40.314][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-13 20:14:40.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:40.316][biodb::testThat]
biodb.INFO [2025-03-13 20:14:40.336][biodb::testThat]
biodb.INFO [2025-03-13 20:14:40.337][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-13 20:14:40.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:40.339][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:40.341][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.343][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.344][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:40.346][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.347][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:40.348][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:40.349][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:40.350][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:40.351][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-03-13 20:14:40.358][biodb::testThat]
biodb.INFO [2025-03-13 20:14:40.359][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-13 20:14:40.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:40.361][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:40.363][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.364][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.366][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:40.367][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:40.368][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:40.369][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:40.370][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:40.371][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:40.372][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-03-13 20:14:40.380][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:40.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:40.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.383][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.384][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:40.385][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:40.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:40.393][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:40.394][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:40.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:40.396][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 20:14:40.397][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 20:14:40.398][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-13 20:14:40.405][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-13 20:14:40.406][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 20:14:40.407][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.409][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.410][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.411][FUN] Functions in observer BiodbConfig: [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 [2025-03-13 20:14:40.415][biodb::testContext]
biodb.INFO [2025-03-13 20:14:40.416][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:40.417][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-03-13 20:14:40.417][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:40.418][biodb::testContext]
biodb.INFO [2025-03-13 20:14:40.422][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-13 20:14:40.424][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 20:14:40.427][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:40.428][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 20:14:40.429][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 20:14:40.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.433][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 20:14:40.434][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 20:14:40.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.437][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 20:14:40.438][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 20:14:40.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.442][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 20:14:40.443][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 20:14:40.444][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 20:14:40.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.447][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 20:14:40.448][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 20:14:40.449][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 20:14:40.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.453][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 20:14:40.454][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 20:14:40.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.457][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 20:14:40.458][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 20:14:40.459][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 20:14:40.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.463][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 20:14:40.464][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 20:14:40.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.467][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 20:14:40.468][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 20:14:40.469][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 20:14:40.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.473][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 20:14:40.473][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 20:14:40.474][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 20:14:40.475][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 20:14:40.476][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 20:14:40.477][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 20:14:40.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.481][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 20:14:40.482][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 20:14:40.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.485][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 20:14:40.486][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 20:14:40.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.490][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 20:14:40.491][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 20:14:40.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.494][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 20:14:40.500][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 20:14:40.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.503][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[2025-03-13 20:14:40.504][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 20:14:40.505][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 20:14:40.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.508][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 20:14:40.509][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 20:14:40.512][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 20:14:40.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.516][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 20:14:40.517][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 20:14:40.518][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 20:14:40.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.521][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 20:14:40.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.524][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-13 20:14:40.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:40.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.529][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.531][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 20:14:40.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:40.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.534][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 20:14:40.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:40.536][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.537][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:40.537][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 20:14:40.537][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 20:14:40.537][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 20:14:40.537][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 20:14:40.539][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:40.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:40.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.544][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.545][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:40.547][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:40.548][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.549][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.550][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 20:14:40.552][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.553][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 20:14:40.554][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:40.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.557][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.559][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 20:14:40.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:40.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.562][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 20:14:40.563][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:40.564][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.565][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.566][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:40.566][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 20:14:40.566][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 20:14:40.566][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 20:14:40.566][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 20:14:40.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:40.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.570][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:40.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.573][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.574][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.575][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:40.576][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:40.577][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.578][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.579][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 20:14:40.581][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.582][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-13 20:14:40.583][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.584][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:40.585][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.586][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.586][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.588][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 20:14:40.589][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:40.590][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.591][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 20:14:40.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:40.593][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.594][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.595][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:40.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:40.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.603][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:40.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:40.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.613][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.614][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 20:14:40.616][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.617][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 20:14:40.618][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.619][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:40.620][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.621][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.622][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.623][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.624][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 20:14:40.625][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:40.626][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.627][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 20:14:40.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:40.629][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.630][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:40.630][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.631][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:40.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.634][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:40.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:40.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:40.637][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:40.638][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.639][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:40.640][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:40.641][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:40.642][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:40.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:40.645][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.758][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 20:14:40.759][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 20:14:40.761][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 20:14:40.762][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 20:14:40.764][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 20:14:40.765][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 20:14:40.767][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 20:14:40.768][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 20:14:40.770][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 20:14:40.771][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 20:14:40.773][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 20:14:40.774][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 20:14:40.776][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 20:14:40.777][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 20:14:40.779][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 20:14:40.780][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 20:14:40.782][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 20:14:40.783][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 20:14:40.784][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 20:14:40.786][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 20:14:40.787][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 20:14:40.789][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 20:14:40.790][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 20:14:40.792][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 20:14:40.793][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 20:14:40.795][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 20:14:40.796][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 20:14:40.798][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 20:14:40.799][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 20:14:40.801][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 20:14:40.802][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 20:14:40.804][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 20:14:40.805][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 20:14:40.807][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 20:14:40.808][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 20:14:40.810][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 20:14:40.811][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 20:14:40.812][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 20:14:40.814][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 20:14:40.815][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 20:14:40.817][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 20:14:40.818][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 20:14:40.820][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 20:14:40.821][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 20:14:40.823][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 20:14:40.824][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 20:14:40.826][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 20:14:40.827][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 20:14:40.829][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 20:14:40.830][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 20:14:40.832][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 20:14:40.833][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 20:14:40.835][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 20:14:40.836][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 20:14:40.837][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 20:14:40.839][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 20:14:40.840][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 20:14:40.841][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 20:14:40.843][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 20:14:40.844][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 20:14:40.845][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 20:14:40.847][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 20:14:40.848][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 20:14:40.850][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 20:14:40.851][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 20:14:40.852][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 20:14:40.860][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 20:14:40.862][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 20:14:40.864][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 20:14:40.865][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 20:14:40.866][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 20:14:40.868][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 20:14:40.869][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 20:14:40.871][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 20:14:40.872][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 20:14:40.873][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 20:14:40.875][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 20:14:40.876][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 20:14:40.877][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 20:14:40.879][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 20:14:40.880][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 20:14:40.881][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 20:14:40.882][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 20:14:40.884][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 20:14:40.886][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-13 20:14:40.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:40.888][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.889][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.926][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[2025-03-13 20:14:40.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.932][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[2025-03-13 20:14:40.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.938][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[2025-03-13 20:14:40.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.967][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[2025-03-13 20:14:40.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.973][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[2025-03-13 20:14:40.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:40.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:40.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:40.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:40.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:40.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:40.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:40.998][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-13 20:14:41.000][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:41.002][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.003][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.004][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:41.006][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.007][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-13 20:14:41.008][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.009][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 20:14:41.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:41.011][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.012][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-13 20:14:41.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-13 20:14:41.014][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-13 20:14:41.015][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.016][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:41.016][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-13 20:14:41.016][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-13 20:14:41.017][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 20:14:41.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:41.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.024][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-13 20:14:41.024][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-13 20:14:41.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:41.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:41.027][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.028][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.029][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-13 20:14:41.030][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 20:14:41.032][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 20:14:41.033][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 20:14:41.035][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 20:14:41.038][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:41.039][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-13 20:14:41.040][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:41.042][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:41.043][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:41.044][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:41.045][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-13 20:14:41.046][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-13 20:14:41.047][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-13 20:14:41.047][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-13 20:14:41.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:41.049][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:41.050][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-13 20:14:41.051][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-13 20:14:41.052][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:41.055][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:41.056][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:41.057][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:41.059][private$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[2025-03-13 20:14:41.060][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:41.061][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-13 20:14:41.063][biodb::testThat]
biodb.INFO [2025-03-13 20:14:41.064][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-03-13 20:14:41.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:41.066][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:41.075][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:41.077][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:41.078][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:41.080][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:41.081][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:41.082][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:41.083][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:41.084][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:41.085][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:41.088][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-13 20:14:41.094][biodb::testThat]
biodb.INFO [2025-03-13 20:14:41.095][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-03-13 20:14:41.096][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:41.097][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:41.099][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-13 20:14:41.100][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-13 20:14:41.101][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:41.103][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-13 20:14:41.105][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-13 20:14:41.106][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 20:14:41.107][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-13 20:14:41.108][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 20:14:41.110][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:41.111][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:41.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:41.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:41.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:41.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.121][FUN] Functions in observer BiodbConfig: [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[2025-03-13 20:14:41.125][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.126][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.133][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.134][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.137][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.141][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.142][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.145][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.149][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.150][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.157][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.158][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.165][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.166][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.172][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.173][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.177][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.184][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.186][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.188][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.193][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.194][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.196][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.197][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.201][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.202][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.208][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:41.209][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:41.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.216][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:41.217][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:41.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.225][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.232][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.233][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.240][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.248][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:41.249][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:41.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.252][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:41.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:41.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:41.257][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:41.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.258][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:41.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:41.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.264][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:41.265][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.268][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:41.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.283][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.291][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:41.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.299][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.303][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.306][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:41.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:41.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.333][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:41.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.348][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:41.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.355][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:41.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.367][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:41.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:41.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.374][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:41.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:41.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.378][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:41.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:41.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:41.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:41.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:41.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:41.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:41.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:41.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:41.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.420][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:41.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:41.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.454][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.457][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.461][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.465][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.469][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:41.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.472][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:41.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:41.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.476][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:41.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:41.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:41.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:41.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.484][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.496][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.503][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:41.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:41.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:41.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:41.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.527][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:41.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:41.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.530][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:41.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:41.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.538][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:41.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:41.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:41.565][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-13 20:14:41.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:41.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:41.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:41.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 20:14:41.583][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 20:14:41.584][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-13 20:14:41.585][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-13 20:14:41.586][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 20:14:41.587][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:41.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:41.588][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.590][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-13 20:14:41.599][biodb::testContext]
biodb.INFO [2025-03-13 20:14:41.600][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:41.601][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-03-13 20:14:41.602][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 20:14:41.603][biodb::testContext]
biodb.INFO [2025-03-13 20:14:41.607][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-13 20:14:41.608][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 20:14:41.612][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:41.613][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 20:14:41.614][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 20:14:41.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.617][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 20:14:41.618][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 20:14:41.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.622][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 20:14:41.623][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 20:14:41.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.626][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 20:14:41.627][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 20:14:41.628][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 20:14:41.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.632][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 20:14:41.633][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 20:14:41.634][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 20:14:41.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.637][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 20:14:41.638][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 20:14:41.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.641][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 20:14:41.642][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 20:14:41.643][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 20:14:41.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.647][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 20:14:41.648][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 20:14:41.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.651][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 20:14:41.652][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 20:14:41.653][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 20:14:41.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.657][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 20:14:41.658][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 20:14:41.659][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 20:14:41.660][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 20:14:41.661][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 20:14:41.662][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 20:14:41.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.665][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 20:14:41.666][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 20:14:41.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.670][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 20:14:41.671][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 20:14:41.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.674][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 20:14:41.675][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 20:14:41.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.679][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 20:14:41.680][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 20:14:41.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.683][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 20:14:41.684][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 20:14:41.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.688][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 20:14:41.689][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 20:14:41.693][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 20:14:41.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.697][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 20:14:41.698][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 20:14:41.699][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 20:14:41.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.707][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 20:14:41.709][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.710][self$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[2025-03-13 20:14:41.711][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.712][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:41.713][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.716][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 20:14:41.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:41.718][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.719][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 20:14:41.720][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:41.721][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.722][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.723][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:41.723][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 20:14:41.723][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 20:14:41.723][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 20:14:41.723][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 20:14:41.724][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:41.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:41.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.730][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:41.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:41.733][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.734][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.735][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 20:14:41.737][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.738][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 20:14:41.739][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.740][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:41.740][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.741][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.743][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.744][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 20:14:41.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:41.746][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.747][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 20:14:41.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:41.749][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.750][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.751][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:41.751][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 20:14:41.751][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 20:14:41.751][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 20:14:41.751][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 20:14:41.752][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:41.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.755][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:41.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.757][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.758][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:41.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:41.761][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.762][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.763][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 20:14:41.765][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.765][self$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[2025-03-13 20:14:41.766][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.767][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:41.768][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.770][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.771][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.772][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 20:14:41.773][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:41.774][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.775][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 20:14:41.776][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:41.777][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.778][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.779][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:41.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:41.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.785][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.786][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.787][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:41.788][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:41.789][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.790][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.791][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 20:14:41.792][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.793][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 20:14:41.794][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:41.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.804][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 20:14:41.805][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:41.806][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.807][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 20:14:41.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:41.809][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.810][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:41.811][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 20:14:41.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:41.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:41.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:41.817][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:41.818][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.819][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:41.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:41.820][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:41.821][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:41.822][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:41.823][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.849][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[2025-03-13 20:14:41.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.858][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[2025-03-13 20:14:41.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.862][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[2025-03-13 20:14:41.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.870][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[2025-03-13 20:14:41.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:41.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:41.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:41.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:41.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:41.897][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 20:14:41.903][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 20:14:41.904][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 20:14:41.906][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 20:14:41.907][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 20:14:41.908][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 20:14:41.910][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 20:14:41.911][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 20:14:41.912][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 20:14:41.913][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 20:14:41.915][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 20:14:41.916][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 20:14:41.917][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 20:14:41.919][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 20:14:41.920][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 20:14:41.921][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 20:14:41.922][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 20:14:41.924][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 20:14:41.925][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 20:14:41.926][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 20:14:41.928][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 20:14:41.929][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 20:14:41.930][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 20:14:41.932][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 20:14:41.933][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 20:14:41.934][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 20:14:41.935][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 20:14:41.937][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 20:14:41.938][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 20:14:41.939][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 20:14:41.941][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 20:14:41.942][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 20:14:41.943][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 20:14:41.945][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 20:14:41.946][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 20:14:41.947][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 20:14:41.949][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 20:14:41.950][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 20:14:41.951][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 20:14:41.952][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 20:14:41.954][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 20:14:41.955][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 20:14:41.956][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 20:14:41.958][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 20:14:41.959][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 20:14:41.960][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 20:14:41.962][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 20:14:41.963][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 20:14:41.964][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 20:14:41.966][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 20:14:41.967][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 20:14:41.968][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 20:14:41.969][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 20:14:41.971][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 20:14:41.972][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 20:14:41.973][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 20:14:41.975][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 20:14:41.976][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 20:14:41.977][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 20:14:41.979][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 20:14:41.980][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 20:14:41.981][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 20:14:41.983][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 20:14:41.984][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 20:14:41.985][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 20:14:41.987][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 20:14:41.988][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 20:14:41.989][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 20:14:41.990][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 20:14:41.992][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 20:14:41.997][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 20:14:41.999][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 20:14:42.000][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 20:14:42.002][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 20:14:42.003][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 20:14:42.004][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 20:14:42.005][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 20:14:42.007][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 20:14:42.008][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 20:14:42.009][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 20:14:42.011][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 20:14:42.012][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 20:14:42.013][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 20:14:42.015][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 20:14:42.016][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-13 20:14:42.017][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 20:14:42.018][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.020][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.020][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[2025-03-13 20:14:42.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.061][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[2025-03-13 20:14:42.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 20:14:42.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.126][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-13 20:14:42.127][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:42.129][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:42.130][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 20:14:42.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:42.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 20:14:42.133][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:42.134][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-13 20:14:42.135][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:42.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 20:14:42.137][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 20:14:42.138][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 20:14:42.139][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:42.140][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-13 20:14:42.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-13 20:14:42.142][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-13 20:14:42.143][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 20:14:42.144][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 20:14:42.144][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-13 20:14:42.144][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-13 20:14:42.145][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 20:14:42.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:42.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:42.147][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 20:14:42.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 20:14:42.149][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 20:14:42.150][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 20:14:42.151][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-13 20:14:42.151][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-13 20:14:42.152][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:42.153][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:42.154][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 20:14:42.155][self$setPropertyValue]
biodb.DEBUG[2025-03-13 20:14:42.156][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-13 20:14:42.157][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 20:14:42.159][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 20:14:42.160][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 20:14:42.162][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 20:14:42.165][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:42.166][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-13 20:14:42.167][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:42.168][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:42.170][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:42.171][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:42.172][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-13 20:14:42.173][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-13 20:14:42.174][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-13 20:14:42.174][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-13 20:14:42.175][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 20:14:42.176][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 20:14:42.176][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-13 20:14:42.177][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-13 20:14:42.178][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-13 20:14:42.180][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:42.181][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:42.182][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:42.183][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-13 20:14:42.184][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 20:14:42.185][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-13 20:14:42.187][biodb::testThat]
biodb.INFO [2025-03-13 20:14:42.187][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2025-03-13 20:14:42.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 20:14:42.194][biodb::testThat]
biodb.DEBUG[2025-03-13 20:14:42.196][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-13 20:14:42.197][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-03-13 20:14:42.198][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-03-13 20:14:42.201][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:42.202][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:42.204][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:42.205][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:42.206][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:42.207][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:42.208][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:42.209][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:42.210][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:42.211][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:42.212][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-03-13 20:14:42.214][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-13 20:14:42.214][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-13 20:14:42.216][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:42.217][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-13 20:14:42.219][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-13 20:14:42.220][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 20:14:42.222][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-13 20:14:42.223][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 20:14:42.224][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:42.226][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:42.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:42.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 20:14:42.240][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.241][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.248][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.249][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.252][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.256][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.257][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.260][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.264][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.265][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.268][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.281][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.282][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.289][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.290][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.293][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.302][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.303][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.306][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.310][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.311][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.313][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.318][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.319][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.326][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.327][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.334][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.335][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.342][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.343][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.350][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.351][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.358][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.366][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.367][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.370][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.374][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.375][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.378][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.382][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:42.384][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:42.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.412][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.416][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.420][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.428][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.462][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.498][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.506][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.509][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.545][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.552][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.579][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.583][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.586][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.590][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.594][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.598][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.605][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.609][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.617][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:42.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.633][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:42.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.657][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:42.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:42.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:42.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:42.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.668][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:42.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:42.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:42.695][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-13 20:14:42.696][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.700][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.704][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:42.711][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:42.712][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:42.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:42.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:42.729][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-13 20:14:42.730][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-13 20:14:42.732][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:42.733][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-13 20:14:42.735][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-13 20:14:42.736][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 20:14:42.738][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-13 20:14:42.739][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 20:14:42.740][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-13 20:14:42.741][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-13 20:14:42.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:42.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:42.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:42.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:42.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:42.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:42.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 20:14:42.754][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.755][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.757][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.762][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.763][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.765][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.766][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:42.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.770][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.771][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.774][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.778][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.779][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.782][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.786][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.787][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.795][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.796][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.803][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:42.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.811][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.812][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.814][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.815][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:42.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.819][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.820][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.823][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:42.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.850][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.852][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:42.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.864][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.865][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.868][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:42.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:42.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.873][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.874][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:42.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:42.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.881][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.882][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:42.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.890][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.891][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:42.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.899][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:42.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:42.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.907][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.908][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.910][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.912][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:42.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:42.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.916][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.917][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:42.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:42.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.924][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:42.925][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-13 20:14:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:42.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:42.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:42.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.950][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.954][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 20:14:42.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.959][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.963][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.971][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-13 20:14:42.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 20:14:42.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-13 20:14:42.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:42.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:42.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:43.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:43.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:43.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:43.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:43.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-13 20:14:43.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:43.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:43.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:43.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:43.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.019][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:43.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-13 20:14:43.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:43.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.026][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:43.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-13 20:14:43.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.038][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.042][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.045][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:43.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:43.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:43.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:43.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 20:14:43.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 20:14:43.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:43.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:43.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:43.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:43.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 20:14:43.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 20:14:43.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.085][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:43.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:43.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.089][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:43.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:43.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.093][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:43.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 20:14:43.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:43.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:43.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:43.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:43.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:43.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 20:14:43.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.119][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:43.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.123][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:43.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:43.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.127][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:43.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-13 20:14:43.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.131][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:43.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:43.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.135][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:43.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.139][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:43.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-13 20:14:43.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:43.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:43.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.147][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:43.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:43.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.151][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 20:14:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 20:14:43.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:43.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.170][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-13 20:14:43.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 20:14:43.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 20:14:43.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 20:14:43.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:43.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.204][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:43.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:43.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.212][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:43.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-13 20:14:43.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 20:14:43.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 20:14:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:43.240][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-13 20:14:43.241][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.245][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.249][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.253][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:43.257][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:43.258][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:43.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:43.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:43.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:43.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:43.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:43.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:43.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:43.274][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-13 20:14:43.275][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-13 20:14:43.276][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-13 20:14:43.278][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:43.279][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:43.281][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:43.282][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:43.283][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:43.289][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:43.290][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:43.291][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:43.292][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:43.293][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:43.294][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-13 20:14:43.296][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.300][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.304][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.308][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.312][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.316][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.319][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:43.323][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:43.324][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:43.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:43.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:43.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:43.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:43.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:43.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:43.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 20:14:43.335][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.339][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.344][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.348][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.351][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.355][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:43.363][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-13 20:14:43.364][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:43.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:43.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:43.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:43.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:43.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:43.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:43.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 20:14:43.378][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-13 20:14:43.379][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-13 20:14:43.380][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-13 20:14:43.382][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:43.383][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:43.385][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-13 20:14:43.386][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-13 20:14:43.387][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-13 20:14:43.388][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-13 20:14:43.389][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-13 20:14:43.390][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-13 20:14:43.395][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-13 20:14:43.396][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-13 20:14:43.397][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-13 20:14:43.400][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.404][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.408][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.412][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.415][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.419][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.423][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:43.427][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-13 20:14:43.428][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-03-13 20:14:43.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:43.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:43.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:43.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:43.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:43.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:43.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 20:14:43.439][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.443][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.447][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.450][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.454][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.458][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 20:14:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-13 20:14:43.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-13 20:14:43.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 20:14:43.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 20:14:43.466][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-13 20:14:43.467][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-13 20:14:43.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 20:14:43.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:43.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:43.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:43.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:43.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:43.477][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.INFO [2025-03-13 20:14:43.483][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 20:14:43.484][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-13 20:14:43.485][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-13 20:14:43.486][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 20:14:43.487][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 20:14:43.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 20:14:43.489][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 20:14:43.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 20:14:43.491][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 20:14:43.491][FUN] Functions in observer 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
8.786 0.479 33.324