Pierrick Roger
| Snapshot Date: 2025-01-19 12:27 -0500 (Sun, 19 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: RELEASE_3_20 |
| git_last_commit: 0eb718c |
| git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-20 12:16 -0500 (Mon, 20 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| 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 204/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbHmdb |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbHmdb_1.12.0.tar.gz |
| StartedAt: 2025-01-19 18:58:05 -0500 (Sun, 19 Jan 2025) |
| EndedAt: 2025-01-19 18:59:02 -0500 (Sun, 19 Jan 2025) |
| EllapsedTime: 57.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbHmdb_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
EntryMaker.hpp:22:14: warning: ‘bool EntryMaker::closed’ [-Wreorder]
EntryMaker.cpp:5:1: warning: when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
libs 6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbHmdb
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘biodbHmdb’ ...
** 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
23 | TagDetector accession_tag;
| ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning: ‘bool EntryMaker::closed’ [-Wreorder]
22 | bool closed;
| ^~~~~~
EntryMaker.cpp:5:1: warning: when initialized here [-Wreorder]
5 | EntryMaker::EntryMaker() :
| ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘biodbHmdb’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-01-19 18:58:36.006][biodb::testContext]
biodb.INFO [2025-01-19 18:58:36.008][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:36.009][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-01-19 18:58:36.010][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:36.011][biodb::testContext]
biodb.INFO [2025-01-19 18:58:36.012][biodb::testThat]
biodb.INFO [2025-01-19 18:58:36.013][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2025-01-19 18:58:36.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:36.015][biodb::testThat]
biodb.INFO [2025-01-19 18:58:36.107][biodb::testContext]
biodb.INFO [2025-01-19 18:58:36.108][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:36.109][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-01-19 18:58:36.110][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:36.111][biodb::testContext]
biodb.INFO [2025-01-19 18:58:36.118][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-19 18:58:36.120][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-19 18:58:36.127][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:36.128][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-19 18:58:36.129][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-19 18:58:36.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.132][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-19 18:58:36.156][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-19 18:58:36.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.159][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-19 18:58:36.160][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-19 18:58:36.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.163][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-19 18:58:36.164][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-19 18:58:36.165][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-19 18:58:36.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.168][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-19 18:58:36.169][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-19 18:58:36.170][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-19 18:58:36.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.173][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-19 18:58:36.174][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-19 18:58:36.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.177][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.DEBUG[2025-01-19 18:58:36.178][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-19 18:58:36.179][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-19 18:58:36.180][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-19 18:58:36.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.183][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-19 18:58:36.184][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-19 18:58:36.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.187][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-19 18:58:36.188][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-19 18:58:36.189][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-19 18:58:36.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.192][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-19 18:58:36.193][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-19 18:58:36.194][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-19 18:58:36.195][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-19 18:58:36.196][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-19 18:58:36.197][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-19 18:58:36.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.200][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-19 18:58:36.201][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-19 18:58:36.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.204][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-19 18:58:36.205][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-19 18:58:36.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.209][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-19 18:58:36.210][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-19 18:58:36.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.213][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-19 18:58:36.214][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-19 18:58:36.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.217][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-19 18:58:36.218][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-19 18:58:36.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.221][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-19 18:58:36.222][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-19 18:58:36.225][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-19 18:58:36.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.229][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-19 18:58:36.230][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-19 18:58:36.231][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-19 18:58:36.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.236][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-19 18:58:36.275][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-19 18:58:36.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.297][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:36.298][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.300][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.302][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-19 18:58:36.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:36.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.305][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-19 18:58:36.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:36.307][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.308][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.309][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:36.309][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-19 18:58:36.309][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-19 18:58:36.309][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-19 18:58:36.309][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-19 18:58:36.310][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:36.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.313][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:36.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.315][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.316][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.317][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.318][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:36.319][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:36.320][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.321][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.322][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-19 18:58:36.324][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.325][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-19 18:58:36.342][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.343][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:36.344][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.345][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.346][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.347][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-19 18:58:36.349][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:36.350][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.351][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-19 18:58:36.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:36.352][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.353][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.354][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:36.354][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-19 18:58:36.354][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-19 18:58:36.354][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-19 18:58:36.354][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-19 18:58:36.356][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:36.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.358][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:36.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.361][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.362][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.363][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:36.364][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:36.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.366][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.367][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-19 18:58:36.369][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.370][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-19 18:58:36.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:36.373][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.375][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.376][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.377][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-19 18:58:36.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:36.380][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.380][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-19 18:58:36.381][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:36.382][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.383][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.384][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:36.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:36.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.392][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:36.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:36.395][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.396][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.397][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-19 18:58:36.399][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.400][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-19 18:58:36.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.402][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:36.403][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.404][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.407][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-19 18:58:36.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:36.409][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.410][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-19 18:58:36.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:36.412][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.413][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.414][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.415][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:36.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:36.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.421][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:36.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:36.424][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.425][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:36.430][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.436][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[2025-01-19 18:58:36.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.440][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[2025-01-19 18:58:36.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.462][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[2025-01-19 18:58:36.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.475][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[2025-01-19 18:58:36.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.479][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[2025-01-19 18:58:36.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.491][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".
biodb.DEBUG[2025-01-19 18:58:36.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.505][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-19 18:58:36.509][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-19 18:58:36.510][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-19 18:58:36.512][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-19 18:58:36.513][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-19 18:58:36.519][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-19 18:58:36.520][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-19 18:58:36.521][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-19 18:58:36.523][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-19 18:58:36.524][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-19 18:58:36.525][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-19 18:58:36.526][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-19 18:58:36.528][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-19 18:58:36.529][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-19 18:58:36.530][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-19 18:58:36.531][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-19 18:58:36.533][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-19 18:58:36.534][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-19 18:58:36.535][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-19 18:58:36.536][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-19 18:58:36.538][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-19 18:58:36.539][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-19 18:58:36.540][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-19 18:58:36.542][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-19 18:58:36.543][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-19 18:58:36.544][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-19 18:58:36.545][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-19 18:58:36.547][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-19 18:58:36.548][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-19 18:58:36.549][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-19 18:58:36.551][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-19 18:58:36.552][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-19 18:58:36.553][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-19 18:58:36.555][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-19 18:58:36.556][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-19 18:58:36.557][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-19 18:58:36.558][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-19 18:58:36.560][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-19 18:58:36.561][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-19 18:58:36.562][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-19 18:58:36.564][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-19 18:58:36.565][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-19 18:58:36.566][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-19 18:58:36.568][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-19 18:58:36.569][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-19 18:58:36.570][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-19 18:58:36.572][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-19 18:58:36.573][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-19 18:58:36.574][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-19 18:58:36.576][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-19 18:58:36.577][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-19 18:58:36.578][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-19 18:58:36.580][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-19 18:58:36.581][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-19 18:58:36.582][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-19 18:58:36.583][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-19 18:58:36.585][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-19 18:58:36.586][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-19 18:58:36.587][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-19 18:58:36.589][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-19 18:58:36.590][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-19 18:58:36.591][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-19 18:58:36.593][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-19 18:58:36.594][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-19 18:58:36.595][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-19 18:58:36.596][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-19 18:58:36.598][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-19 18:58:36.599][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-19 18:58:36.600][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-19 18:58:36.602][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-19 18:58:36.603][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-19 18:58:36.604][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-19 18:58:36.606][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-19 18:58:36.607][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-19 18:58:36.608][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-19 18:58:36.609][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-19 18:58:36.611][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-19 18:58:36.612][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-19 18:58:36.613][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-19 18:58:36.615][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-19 18:58:36.616][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-19 18:58:36.617][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-19 18:58:36.619][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-19 18:58:36.624][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-19 18:58:36.626][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-19 18:58:36.629][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:36.630][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.631][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.641][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[2025-01-19 18:58:36.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.664][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[2025-01-19 18:58:36.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.669][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[2025-01-19 18:58:36.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.704][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[2025-01-19 18:58:36.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.710][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[2025-01-19 18:58:36.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.715][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[2025-01-19 18:58:36.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.721][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[2025-01-19 18:58:36.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.726][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[2025-01-19 18:58:36.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.732][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[2025-01-19 18:58:36.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:36.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:36.761][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-19 18:58:36.771][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:36.772][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.773][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.775][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:36.776][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.777][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-19 18:58:36.778][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.779][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.780][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-19 18:58:36.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:36.781][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.782][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-19 18:58:36.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-19 18:58:36.784][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-19 18:58:36.785][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:36.786][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:36.786][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-19 18:58:36.786][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-19 18:58:36.787][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-19 18:58:36.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.790][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:36.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:36.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:36.792][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:36.793][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-19 18:58:36.793][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-19 18:58:36.794][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:36.795][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:36.796][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:36.796][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:36.802][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-19 18:58:36.803][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-19 18:58:36.805][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-19 18:58:36.806][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-19 18:58:36.808][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-19 18:58:36.829][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:36.830][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-19 18:58:36.834][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:36.837][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:36.841][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:36.842][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:36.843][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-19 18:58:36.844][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-01-19 18:58:36.845][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-19 18:58:36.845][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-01-19 18:58:36.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:36.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:36.848][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-01-19 18:58:36.849][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-01-19 18:58:36.850][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:36.872][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:36.873][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:36.874][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:36.875][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:36.876][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:36.877][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-01-19 18:58:36.885][biodb::testThat]
biodb.INFO [2025-01-19 18:58:36.885][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-01-19 18:58:36.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:36.887][biodb::testThat]
biodb.TRACE[2025-01-19 18:58:36.915][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-01-19 18:58:36.917][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:36.920][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:36.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:36.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:36.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:36.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:36.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:36.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:36.936][FUN] Functions in observer BiodbConfig: [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[2025-01-19 18:58:36.946][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:36.947][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:36.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:36.949][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:36.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:36.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:36.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:36.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:36.966][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:36.967][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:36.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:36.969][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:36.993][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:36.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:36.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:36.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:36.997][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:36.998][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:36.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.000][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.001][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.005][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.005][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.007][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.008][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.015][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.020][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.021][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.022][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.027][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.028][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.030][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.031][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.035][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.036][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.038][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.039][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.049][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.050][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.052][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.057][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.058][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.059][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.064][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.065][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.067][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.072][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.073][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.075][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.082][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.087][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.088][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.090][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.095][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.096][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.098][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.103][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.104][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.105][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.106][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.110][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.111][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.113][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.118][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:37.119][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.121][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.122][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:37.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.167][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.175][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.179][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.182][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.186][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.189][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:37.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.229][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.248][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.251][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.255][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.258][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.292][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.295][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.329][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.332][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.340][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.343][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.347][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.350][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.358][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.361][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:37.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.376][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:37.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.414][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.418][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.425][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:37.454][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-19 18:58:37.456][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-19 18:58:37.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-19 18:58:37.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-19 18:58:37.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-19 18:58:37.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.464][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-19 18:58:37.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-19 18:58:37.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.467][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-19 18:58:37.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-19 18:58:37.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.492][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.525][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.529][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:37.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.551][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.553][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:37.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:37.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.569][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.572][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.581][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.582][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.583][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.584][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:37.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.606][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.607][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.609][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:37.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.620][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.628][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.631][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.632][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.634][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:37.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.657][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.658][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.659][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:37.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.682][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.683][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.685][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:37.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.707][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.708][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.714][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:37.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:37.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.726][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.730][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.733][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.737][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.738][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.740][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.741][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:37.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:37.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.763][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.764][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.765][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:37.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:37.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.777][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.781][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.784][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.788][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.789][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.791][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.792][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:37.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.813][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.814][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.816][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.838][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.839][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.841][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.868][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.869][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.870][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.871][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:37.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.886][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.893][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.894][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.896][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.897][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:37.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.907][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.916][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.924][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.925][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.926][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.927][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:37.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:37.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.981][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.982][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.984][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:37.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:37.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:37.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:37.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:37.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.007][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.008][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.010][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.026][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.029][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.036][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.037][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.039][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.040][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.050][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.052][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.053][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.057][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.058][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.060][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.064][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.065][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.067][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.071][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.072][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.073][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.077][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.078][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.080][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.084][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.085][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.087][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.091][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.092][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.093][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.097][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.098][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.100][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.104][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.105][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.107][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.111][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:38.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:38.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.113][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.117][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:38.118][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:38.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.120][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.124][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.126][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.130][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.131][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.133][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.137][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.139][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.143][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.146][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.154][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.155][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.157][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.161][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.162][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.164][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.168][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:38.169][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:38.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.170][ef$get] fields variable is a list.
biodb.INFO [2025-01-19 18:58:38.177][biodb::testThat]
biodb.INFO [2025-01-19 18:58:38.178][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-19 18:58:38.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:38.180][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:38.193][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-19 18:58:38.200][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-19 18:58:38.204][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.206][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-19 18:58:38.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-19 18:58:38.209][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-19 18:58:38.212][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-19 18:58:38.213][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-19 18:58:38.236][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:38.237][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:38.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:38.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:38.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:38.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:38.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:38.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:38.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-19 18:58:38.251][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.252][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.254][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.259][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.260][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.261][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.263][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.266][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.267][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.269][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.270][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.274][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.275][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.277][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.278][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.289][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.294][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.295][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.297][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.302][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.303][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.304][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.305][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.309][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.310][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.312][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.313][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.317][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.318][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.320][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.325][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.326][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.327][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.332][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:38.333][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:38.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.335][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:38.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:38.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.340][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:38.341][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:38.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.343][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:38.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:38.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.350][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.356][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.357][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.358][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.364][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.366][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.371][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.372][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.374][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.375][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.378][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:38.379][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:38.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.381][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.382][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:38.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:38.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.386][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:38.387][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.389][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.390][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:38.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.405][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.408][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.412][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:38.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.420][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.423][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.427][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:38.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.456][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:38.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.463][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:38.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.478][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:38.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.485][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.488][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.492][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:38.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:38.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:38.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:38.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:38.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:38.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:38.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:38.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:38.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:38.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:38.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.528][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.532][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.535][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:38.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:38.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.565][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.572][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:38.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.576][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.580][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.583][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.587][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:38.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:38.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.591][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:38.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:38.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.594][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:38.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:38.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.598][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:38.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:38.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:38.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.635][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:38.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:38.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.638][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:38.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:38.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.646][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:38.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:38.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:38.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:38.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.675][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-19 18:58:38.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-19 18:58:38.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-19 18:58:38.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-19 18:58:38.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-19 18:58:38.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-19 18:58:38.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-19 18:58:38.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-19 18:58:38.693][biodb::testThat]
biodb.INFO [2025-01-19 18:58:38.694][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-19 18:58:38.695][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:38.696][biodb::testThat]
biodb.TRACE[2025-01-19 18:58:38.699][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.700][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.701][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.703][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-01-19 18:58:38.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.740][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-01-19 18:58:38.741][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-19 18:58:38.742][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-19 18:58:38.743][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-19 18:58:38.745][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.746][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.747][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:38.748][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.749][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:38.751][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:38.752][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:38.753][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:38.753][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:38.754][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:38.755][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-19 18:58:38.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:38.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.772][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:38.772][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:38.773][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-19 18:58:38.784][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.785][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.787][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.788][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-01-19 18:58:38.801][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.805][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.809][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.814][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[2025-01-19 18:58:38.864][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-19 18:58:38.865][private$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[2025-01-19 18:58:38.866][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-19 18:58:38.879][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.881][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.882][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:38.883][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.884][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:38.898][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:38.899][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:38.900][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:38.901][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:38.902][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:38.903][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-19 18:58:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.912][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.919][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:38.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.923][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:38.923][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:38.924][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-19 18:58:38.935][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.936][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.937][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.939][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-01-19 18:58:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.952][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.956][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.962][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-01-19 18:58:38.963][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-01-19 18:58:38.964][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-19 18:58:38.965][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-19 18:58:38.966][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.967][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.969][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:38.970][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:38.971][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:38.972][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:38.973][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:38.974][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:38.975][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:38.976][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:38.976][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-19 18:58:38.978][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.982][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.985][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:38.989][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:38.992][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:38.993][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:38.994][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-01-19 18:58:39.007][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.008][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-01-19 18:58:39.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:39.009][biodb::testThat]
biodb.TRACE[2025-01-19 18:58:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:39.042][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-19 18:58:39.043][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-19 18:58:39.044][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-19 18:58:39.046][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:39.047][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:39.048][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:39.049][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:39.050][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:39.051][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:39.052][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:39.053][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:39.054][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:39.055][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:39.056][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-19 18:58:39.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.061][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:39.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:39.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:39.072][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:39.073][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-01-19 18:58:39.086][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.087][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-01-19 18:58:39.087][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:39.088][biodb::testThat]
biodb.TRACE[2025-01-19 18:58:39.106][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-19 18:58:39.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-19 18:58:39.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-19 18:58:39.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-19 18:58:39.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-19 18:58:39.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.170][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-19 18:58:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-19 18:58:39.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:39.174][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-19 18:58:39.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-19 18:58:39.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:39.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-19 18:58:39.183][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.183][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-19 18:58:39.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:39.185][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.192][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.193][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-19 18:58:39.194][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:39.195][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.201][biodb::testThat]
biodb.INFO [2025-01-19 18:58:39.202][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-19 18:58:39.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:39.204][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:39.207][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-01-19 18:58:48.354][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-01-19 18:58:48.439][biodb::testThat]
biodb.INFO [2025-01-19 18:58:48.441][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-19 18:58:48.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:48.444][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:49.288][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-01-19 18:58:51.370][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:51.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:51.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.376][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.378][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:51.380][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:51.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.383][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.385][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:51.386][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:51.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.389][ef$get] fields variable is a list.
biodb.INFO [2025-01-19 18:58:51.393][biodb::testThat]
biodb.INFO [2025-01-19 18:58:51.394][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-01-19 18:58:51.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:51.397][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:51.401][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-01-19 18:58:51.494][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-01-19 18:58:51.496][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-01-19 18:58:51.497][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-01-19 18:58:51.498][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-01-19 18:58:51.499][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-01-19 18:58:51.501][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-01-19 18:58:51.502][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-01-19 18:58:51.504][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-01-19 18:58:51.505][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-01-19 18:58:51.506][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-01-19 18:58:51.508][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker23b8c0735ee353marker".
biodb.TRACE[2025-01-19 18:58:51.509][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-01-19 18:58:51.510][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-01-19 18:58:51.511][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-01-19 18:58:51.513][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-01-19 18:58:51.514][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2025-01-19 18:58:51.515][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-01-19 18:58:51.516][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2025-01-19 18:58:51.524][private$findXmlDatabaseFile] Found files [2]: "101823bb877d774b32.tsv, hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2025-01-19 18:58:51.525][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-01-19 18:58:51.526][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-01-19 18:58:51.528][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2025-01-19 18:58:51.535][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2025-01-19 18:58:51.536][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-01-19 18:58:51.537][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-01-19 18:58:51.538][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-01-19 18:58:51.540][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker23b8c02b3ff081marker".
biodb.TRACE[2025-01-19 18:58:51.541][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-01-19 18:58:51.542][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-01-19 18:58:51.557][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-01-19 18:58:51.559][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-19 18:58:51.560][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-19 18:58:51.561][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-19 18:58:51.562][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.563][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:51.565][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:51.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:51.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:51.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:51.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:51.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:51.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-19 18:58:51.576][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.611][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:51.637][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-01-19 18:58:51.638][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-01-19 18:58:51.653][biodb::testThat]
biodb.INFO [2025-01-19 18:58:51.654][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-01-19 18:58:51.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:51.656][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:51.663][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-01-19 18:58:51.664][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-01-19 18:58:51.665][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-19 18:58:51.666][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.668][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-19 18:58:51.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-01-19 18:58:51.671][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-19 18:58:51.672][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-19 18:58:51.673][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-19 18:58:51.674][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.675][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:51.676][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:51.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:51.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:51.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:51.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:51.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:51.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.686][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.TRACE[2025-01-19 18:58:51.688][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.691][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:51.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:51.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:51.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:51.722][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-01-19 18:58:51.723][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-01-19 18:58:51.724][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-01-19 18:58:51.735][biodb::testThat]
biodb.INFO [2025-01-19 18:58:51.736][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-01-19 18:58:51.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:51.738][biodb::testThat]
biodb.INFO [2025-01-19 18:58:51.758][biodb::testThat]
biodb.INFO [2025-01-19 18:58:51.759][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-01-19 18:58:51.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:51.761][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:51.763][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.764][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.766][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:51.767][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.768][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:51.769][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:51.770][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:51.771][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:51.772][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-01-19 18:58:51.779][biodb::testThat]
biodb.INFO [2025-01-19 18:58:51.780][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-01-19 18:58:51.781][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:51.781][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:51.784][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.785][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.786][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:51.788][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:51.789][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:51.790][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:51.791][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:51.792][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:51.793][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-01-19 18:58:51.800][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:51.802][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:51.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.803][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.804][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:51.805][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:51.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.807][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:51.808][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:51.809][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:51.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:51.811][ef$get] fields variable is a list.
biodb.INFO [2025-01-19 18:58:51.812][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-19 18:58:51.813][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-19 18:58:51.825][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-19 18:58:51.826][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-19 18:58:51.827][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:51.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:51.829][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:51.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:51.830][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-19 18:58:51.834][biodb::testContext]
biodb.INFO [2025-01-19 18:58:51.835][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:51.836][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-01-19 18:58:51.837][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:51.838][biodb::testContext]
biodb.INFO [2025-01-19 18:58:51.841][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-19 18:58:51.843][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-19 18:58:51.846][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:51.847][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-19 18:58:51.848][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-19 18:58:51.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.852][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-19 18:58:51.853][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-19 18:58:51.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.856][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-19 18:58:51.857][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-19 18:58:51.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.860][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-19 18:58:51.861][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-19 18:58:51.862][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-19 18:58:51.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.866][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-19 18:58:51.867][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-19 18:58:51.868][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-19 18:58:51.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.871][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-19 18:58:51.872][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-19 18:58:51.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.874][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[2025-01-19 18:58:51.875][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-19 18:58:51.876][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-19 18:58:51.877][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-19 18:58:51.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.880][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-19 18:58:51.881][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-19 18:58:51.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.885][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-19 18:58:51.886][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-19 18:58:51.887][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-19 18:58:51.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.890][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-19 18:58:51.891][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-19 18:58:51.892][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-19 18:58:51.893][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-19 18:58:51.893][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-19 18:58:51.894][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-19 18:58:51.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.897][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[2025-01-19 18:58:51.898][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-19 18:58:51.899][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-19 18:58:51.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.902][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-19 18:58:51.903][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-19 18:58:51.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.906][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-19 18:58:51.907][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-19 18:58:51.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.911][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-19 18:58:51.912][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-19 18:58:51.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.914][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[2025-01-19 18:58:51.915][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-19 18:58:51.916][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-19 18:58:51.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.924][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-19 18:58:51.925][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-19 18:58:51.929][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-19 18:58:51.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.932][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[2025-01-19 18:58:51.933][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-19 18:58:51.934][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-19 18:58:51.935][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-19 18:58:51.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:51.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:51.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:51.938][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-19 18:58:51.940][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:51.941][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-19 18:58:51.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:51.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:51.945][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:51.946][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:51.947][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-19 18:58:51.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:51.949][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.950][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-19 18:58:51.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:51.952][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:51.953][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.954][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:51.954][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-19 18:58:51.954][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-19 18:58:51.954][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-19 18:58:51.954][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-19 18:58:51.955][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:51.956][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:51.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:51.957][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:51.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:51.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:51.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:51.961][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:51.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:51.962][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:51.963][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:51.964][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:51.965][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-19 18:58:51.967][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:51.968][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-19 18:58:51.969][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.970][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:51.971][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.972][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:51.972][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:51.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:51.974][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-19 18:58:51.975][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:51.976][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.977][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-19 18:58:51.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:51.979][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:51.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.981][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:51.981][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-19 18:58:51.981][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-19 18:58:51.981][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-19 18:58:51.981][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-19 18:58:51.982][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:51.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:51.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:51.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:51.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:51.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:51.987][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:51.988][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:51.989][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:51.990][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:51.990][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:51.991][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:51.992][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-19 18:58:51.994][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.995][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-19 18:58:51.996][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:51.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:51.999][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.000][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.001][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.002][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-19 18:58:52.002][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:52.003][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.004][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-19 18:58:52.005][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:52.006][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.007][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.008][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:52.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:52.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:52.011][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:52.012][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:52.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:52.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.015][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:52.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:52.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.018][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.020][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-19 18:58:52.021][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.027][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-19 18:58:52.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:52.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.031][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.034][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-19 18:58:52.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:52.035][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.036][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-19 18:58:52.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:52.038][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.040][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.041][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:52.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:52.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:52.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:52.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:52.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:52.046][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.047][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:52.049][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:52.049][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.050][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.052][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:52.052][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.107][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[2025-01-19 18:58:52.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.129][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-19 18:58:52.130][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-19 18:58:52.132][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-19 18:58:52.133][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-19 18:58:52.134][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-19 18:58:52.136][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-19 18:58:52.137][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-19 18:58:52.138][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-19 18:58:52.139][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-19 18:58:52.141][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-19 18:58:52.142][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-19 18:58:52.143][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-19 18:58:52.144][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-19 18:58:52.146][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-19 18:58:52.147][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-19 18:58:52.148][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-19 18:58:52.149][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-19 18:58:52.151][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-19 18:58:52.152][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-19 18:58:52.153][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-19 18:58:52.155][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-19 18:58:52.156][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-19 18:58:52.157][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-19 18:58:52.158][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-19 18:58:52.160][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-19 18:58:52.161][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-19 18:58:52.162][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-19 18:58:52.163][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-19 18:58:52.165][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-19 18:58:52.166][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-19 18:58:52.167][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-19 18:58:52.169][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-19 18:58:52.170][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-19 18:58:52.171][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-19 18:58:52.172][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-19 18:58:52.174][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-19 18:58:52.175][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-19 18:58:52.176][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-19 18:58:52.177][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-19 18:58:52.179][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-19 18:58:52.180][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-19 18:58:52.181][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-19 18:58:52.183][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-19 18:58:52.184][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-19 18:58:52.185][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-19 18:58:52.186][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-19 18:58:52.188][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-19 18:58:52.189][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-19 18:58:52.190][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-19 18:58:52.192][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-19 18:58:52.193][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-19 18:58:52.194][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-19 18:58:52.195][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-19 18:58:52.197][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-19 18:58:52.198][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-19 18:58:52.199][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-19 18:58:52.201][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-19 18:58:52.202][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-19 18:58:52.203][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-19 18:58:52.204][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-19 18:58:52.206][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-19 18:58:52.207][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-19 18:58:52.208][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-19 18:58:52.209][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-19 18:58:52.211][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-19 18:58:52.212][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-19 18:58:52.213][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-19 18:58:52.214][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-19 18:58:52.216][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-19 18:58:52.217][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-19 18:58:52.218][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-19 18:58:52.224][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-19 18:58:52.226][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-19 18:58:52.227][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-19 18:58:52.228][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-19 18:58:52.229][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-19 18:58:52.231][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-19 18:58:52.232][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-19 18:58:52.233][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-19 18:58:52.234][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-19 18:58:52.236][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-19 18:58:52.237][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-19 18:58:52.238][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-19 18:58:52.239][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-19 18:58:52.241][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-19 18:58:52.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:52.243][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.244][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.348][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-19 18:58:52.350][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:52.352][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.352][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.353][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.354][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:52.355][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.356][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-19 18:58:52.357][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.359][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-19 18:58:52.360][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:52.361][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.362][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-19 18:58:52.363][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-19 18:58:52.365][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:52.365][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:52.365][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-19 18:58:52.365][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-19 18:58:52.366][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-19 18:58:52.367][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:52.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:52.369][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:52.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:52.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:52.372][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:52.372][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-19 18:58:52.372][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-19 18:58:52.373][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:52.374][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:52.375][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:52.376][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:52.377][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-19 18:58:52.379][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-19 18:58:52.380][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-19 18:58:52.382][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-19 18:58:52.383][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-19 18:58:52.386][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:52.387][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-19 18:58:52.388][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:52.389][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:52.391][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:52.391][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:52.393][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-19 18:58:52.394][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-01-19 18:58:52.395][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-19 18:58:52.395][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-01-19 18:58:52.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:52.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:52.397][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-01-19 18:58:52.398][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-01-19 18:58:52.399][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:52.400][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:52.401][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:52.402][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:52.404][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:52.405][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:52.406][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-01-19 18:58:52.407][biodb::testThat]
biodb.INFO [2025-01-19 18:58:52.408][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-01-19 18:58:52.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:52.410][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:52.413][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:52.415][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:52.416][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:52.421][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:52.422][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:52.424][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:52.425][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:52.426][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:52.427][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:52.429][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-01-19 18:58:52.434][biodb::testThat]
biodb.INFO [2025-01-19 18:58:52.435][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-01-19 18:58:52.435][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:52.436][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:52.438][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-01-19 18:58:52.439][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-19 18:58:52.440][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:52.442][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-19 18:58:52.443][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-01-19 18:58:52.445][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-19 18:58:52.446][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-01-19 18:58:52.447][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-19 18:58:52.448][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:52.449][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:52.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:52.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.459][FUN] Functions in observer BiodbConfig: [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[2025-01-19 18:58:52.462][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.465][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.470][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.471][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.472][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.477][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.478][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.480][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.481][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.485][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.486][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.488][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.489][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.494][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.495][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.500][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.501][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.503][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.508][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.509][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.511][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.512][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.516][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.517][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.518][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.520][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.528][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.529][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.531][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.536][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.537][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.539][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.544][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:52.545][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:52.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.547][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.551][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:52.552][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:52.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.554][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:52.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:52.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.559][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.560][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.562][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.568][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.570][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.575][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.577][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.582][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:52.583][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:52.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.585][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.586][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:52.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:52.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.590][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:52.591][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:52.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.593][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.594][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:52.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:52.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.598][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:52.599][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.600][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.616][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.620][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.628][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:52.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.632][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.636][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.639][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:52.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:52.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:52.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:52.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:52.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:52.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.702][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:52.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.705][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:52.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:52.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:52.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:52.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:52.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:52.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:52.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:52.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:52.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:52.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.749][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.753][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:52.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:52.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.779][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.786][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:52.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.790][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.793][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.797][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:52.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:52.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.804][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:52.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:52.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:52.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:52.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.812][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:52.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.843][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:52.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:52.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:52.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:52.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.871][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:52.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:52.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.875][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:52.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:52.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.883][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:52.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:52.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:52.912][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-01-19 18:58:52.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:52.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:52.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-19 18:58:52.932][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-19 18:58:52.933][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-19 18:58:52.934][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-19 18:58:52.935][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-19 18:58:52.936][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:52.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:52.938][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:52.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:52.940][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-19 18:58:52.944][biodb::testContext]
biodb.INFO [2025-01-19 18:58:52.956][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:52.957][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-01-19 18:58:52.958][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-19 18:58:52.959][biodb::testContext]
biodb.INFO [2025-01-19 18:58:52.963][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-19 18:58:52.965][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-19 18:58:52.968][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:52.969][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-19 18:58:52.970][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-19 18:58:52.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.973][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[2025-01-19 18:58:52.973][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-19 18:58:52.974][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-19 18:58:52.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.978][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-19 18:58:52.979][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-19 18:58:52.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.982][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-19 18:58:52.983][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-19 18:58:52.984][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-19 18:58:52.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.987][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-19 18:58:52.988][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-19 18:58:52.989][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-19 18:58:52.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.992][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-19 18:58:52.993][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-19 18:58:52.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:52.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:52.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:52.997][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-19 18:58:52.998][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-19 18:58:52.999][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-19 18:58:52.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.001][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[2025-01-19 18:58:53.002][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-19 18:58:53.003][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-19 18:58:53.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.006][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-19 18:58:53.007][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-19 18:58:53.008][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-19 18:58:53.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.011][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-19 18:58:53.012][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-19 18:58:53.013][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-19 18:58:53.014][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-19 18:58:53.015][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-19 18:58:53.016][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-19 18:58:53.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.019][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-19 18:58:53.020][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-19 18:58:53.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.023][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-19 18:58:53.024][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-19 18:58:53.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.028][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-19 18:58:53.029][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-19 18:58:53.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.032][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-19 18:58:53.033][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-19 18:58:53.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.036][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-19 18:58:53.037][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-19 18:58:53.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.040][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-19 18:58:53.041][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-19 18:58:53.044][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-19 18:58:53.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.047][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-19 18:58:53.048][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-19 18:58:53.049][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-19 18:58:53.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.053][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-19 18:58:53.059][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.060][self$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[2025-01-19 18:58:53.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.062][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:53.063][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.064][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.065][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.067][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-19 18:58:53.067][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:53.068][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.069][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-19 18:58:53.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:53.071][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.072][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.073][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:53.073][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-19 18:58:53.073][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-19 18:58:53.073][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-19 18:58:53.073][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-19 18:58:53.074][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:53.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:53.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.079][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.080][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.081][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:53.082][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:53.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.083][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.084][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-19 18:58:53.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.087][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-19 18:58:53.088][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.089][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:53.090][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.092][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.093][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-19 18:58:53.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:53.095][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.096][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-19 18:58:53.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:53.098][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.099][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:53.100][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-19 18:58:53.100][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-19 18:58:53.100][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-19 18:58:53.100][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-19 18:58:53.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:53.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:53.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.106][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.107][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.108][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:53.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:53.109][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.110][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.111][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-19 18:58:53.113][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.114][self$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[2025-01-19 18:58:53.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:53.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.119][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.120][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-19 18:58:53.121][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:53.122][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.123][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-19 18:58:53.124][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:53.125][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.127][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.128][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:53.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.131][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:53.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.133][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.134][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.135][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:53.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:53.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.138][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.139][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-19 18:58:53.141][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.142][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-19 18:58:53.143][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.143][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:53.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.146][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.148][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-19 18:58:53.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:53.150][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.157][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-19 18:58:53.158][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:53.160][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.161][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.162][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.163][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-19 18:58:53.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.165][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:53.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.169][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.170][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:53.171][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:53.171][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.172][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.174][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:53.174][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.246][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-19 18:58:53.247][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-19 18:58:53.248][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-19 18:58:53.254][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-19 18:58:53.256][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-19 18:58:53.257][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-19 18:58:53.258][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-19 18:58:53.259][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-19 18:58:53.261][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-19 18:58:53.262][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-19 18:58:53.263][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-19 18:58:53.265][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-19 18:58:53.266][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-19 18:58:53.267][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-19 18:58:53.268][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-19 18:58:53.270][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-19 18:58:53.271][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-19 18:58:53.272][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-19 18:58:53.273][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-19 18:58:53.275][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-19 18:58:53.276][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-19 18:58:53.277][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-19 18:58:53.279][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-19 18:58:53.280][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-19 18:58:53.281][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-19 18:58:53.282][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-19 18:58:53.284][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-19 18:58:53.285][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-19 18:58:53.286][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-19 18:58:53.287][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-19 18:58:53.289][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-19 18:58:53.290][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-19 18:58:53.291][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-19 18:58:53.292][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-19 18:58:53.294][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-19 18:58:53.295][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-19 18:58:53.296][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-19 18:58:53.298][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-19 18:58:53.299][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-19 18:58:53.300][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-19 18:58:53.301][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-19 18:58:53.303][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-19 18:58:53.304][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-19 18:58:53.305][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-19 18:58:53.306][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-19 18:58:53.308][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-19 18:58:53.309][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-19 18:58:53.310][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-19 18:58:53.312][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-19 18:58:53.313][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-19 18:58:53.314][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-19 18:58:53.315][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-19 18:58:53.317][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-19 18:58:53.318][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-19 18:58:53.319][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-19 18:58:53.321][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-19 18:58:53.322][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-19 18:58:53.323][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-19 18:58:53.324][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-19 18:58:53.326][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-19 18:58:53.327][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-19 18:58:53.328][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-19 18:58:53.329][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-19 18:58:53.331][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-19 18:58:53.332][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-19 18:58:53.333][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-19 18:58:53.334][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-19 18:58:53.336][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-19 18:58:53.337][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-19 18:58:53.338][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-19 18:58:53.339][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-19 18:58:53.341][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-19 18:58:53.346][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-19 18:58:53.348][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-19 18:58:53.349][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-19 18:58:53.351][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-19 18:58:53.352][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-19 18:58:53.353][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-19 18:58:53.354][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-19 18:58:53.355][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-19 18:58:53.357][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-19 18:58:53.358][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-19 18:58:53.359][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-19 18:58:53.361][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-19 18:58:53.362][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-19 18:58:53.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-19 18:58:53.364][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.365][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.411][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[2025-01-19 18:58:53.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.428][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[2025-01-19 18:58:53.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.434][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[2025-01-19 18:58:53.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.445][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[2025-01-19 18:58:53.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.456][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[2025-01-19 18:58:53.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.462][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[2025-01-19 18:58:53.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-19 18:58:53.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:53.469][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-19 18:58:53.470][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:53.472][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.473][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-19 18:58:53.476][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.477][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-19 18:58:53.478][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.479][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-19 18:58:53.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-19 18:58:53.481][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.482][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-19 18:58:53.483][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-19 18:58:53.484][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-19 18:58:53.485][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-19 18:58:53.486][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-19 18:58:53.486][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-19 18:58:53.486][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-19 18:58:53.487][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-19 18:58:53.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-19 18:58:53.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-19 18:58:53.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-19 18:58:53.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-19 18:58:53.493][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-19 18:58:53.493][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-19 18:58:53.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:53.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:53.496][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-19 18:58:53.497][self$setPropertyValue]
biodb.DEBUG[2025-01-19 18:58:53.498][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-19 18:58:53.499][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-19 18:58:53.501][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-19 18:58:53.502][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-19 18:58:53.503][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-19 18:58:53.506][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:53.507][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-19 18:58:53.508][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:53.510][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:53.511][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:53.512][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:53.513][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-19 18:58:53.514][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-01-19 18:58:53.515][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-19 18:58:53.515][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-01-19 18:58:53.516][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-19 18:58:53.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-19 18:58:53.518][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-01-19 18:58:53.518][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-01-19 18:58:53.519][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-19 18:58:53.521][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:53.522][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:53.523][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:53.524][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-19 18:58:53.525][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-19 18:58:53.526][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-01-19 18:58:53.527][biodb::testThat]
biodb.INFO [2025-01-19 18:58:53.528][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2025-01-19 18:58:53.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-19 18:58:53.530][biodb::testThat]
biodb.DEBUG[2025-01-19 18:58:53.537][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-19 18:58:53.538][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-01-19 18:58:53.539][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-01-19 18:58:53.542][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:53.543][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:53.544][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:53.546][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:53.546][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:53.548][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:53.549][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:53.549][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:53.550][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:53.551][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:53.552][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-01-19 18:58:53.554][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-19 18:58:53.555][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-19 18:58:53.556][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:53.557][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-19 18:58:53.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-19 18:58:53.560][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-19 18:58:53.562][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-19 18:58:53.563][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-19 18:58:53.564][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:53.565][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:53.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:53.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:53.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:53.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:53.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:53.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:53.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-19 18:58:53.579][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.580][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.582][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.586][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.587][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.589][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.591][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.594][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.595][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.597][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.602][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.603][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.605][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.606][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.610][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.611][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.612][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.617][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.618][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.620][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.625][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.628][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.633][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.638][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.640][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.645][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.646][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.648][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.652][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.653][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.655][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.656][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.660][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:53.661][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:53.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.663][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:53.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.668][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:53.669][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:53.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.670][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:53.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.675][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.676][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.678][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.683][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.684][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.685][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.690][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.691][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.693][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.698][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:53.699][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:53.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.701][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.705][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:53.706][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:53.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.708][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.709][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:53.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.713][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:53.714][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.716][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.717][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:53.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.760][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:53.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:53.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:53.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.808][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:53.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.819][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:53.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:53.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.823][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.826][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:53.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:53.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:53.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:53.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:53.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:53.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:53.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:53.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:53.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:53.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:53.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.868][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.875][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:53.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:53.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.901][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.905][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.912][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.916][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:53.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:53.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:53.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.927][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:53.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:53.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:53.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:53.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.934][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.954][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:53.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:53.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:53.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.977][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:53.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:53.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.981][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:53.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:53.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.988][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:53.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:53.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:53.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:53.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:53.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:53.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.014][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-19 18:58:54.015][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.019][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.023][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.026][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.030][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:54.031][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:54.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:54.048][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-01-19 18:58:54.049][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-19 18:58:54.051][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.052][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-19 18:58:54.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-01-19 18:58:54.055][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-19 18:58:54.056][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-01-19 18:58:54.057][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-19 18:58:54.059][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-19 18:58:54.060][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-19 18:58:54.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-19 18:58:54.073][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.074][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.075][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.080][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.081][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.083][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.088][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.089][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.091][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.092][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.096][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.097][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.099][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.100][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.107][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.112][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.113][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.114][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.122][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.127][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.128][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.130][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.131][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.135][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.136][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.138][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.147][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.149][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.151][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.157][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:54.158][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:54.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.160][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:54.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:54.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.165][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:54.166][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:54.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.167][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:54.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:54.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.173][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.174][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.176][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.181][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.184][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.189][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.190][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.191][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.196][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.197][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.199][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.200][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.204][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:54.205][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:54.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.207][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.208][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:54.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:54.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.212][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:54.213][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.215][ef$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.217][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-19 18:58:54.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.231][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-19 18:58:54.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.242][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.246][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-19 18:58:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-19 18:58:54.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-19 18:58:54.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.281][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-19 18:58:54.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.292][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.296][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-19 18:58:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.307][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-19 18:58:54.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.315][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.318][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.322][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:54.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:54.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-19 18:58:54.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-19 18:58:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:54.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:54.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-19 18:58:54.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-19 18:58:54.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.366][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.369][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.373][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-19 18:58:54.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-19 18:58:54.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.399][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.403][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-19 18:58:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.418][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-19 18:58:54.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:54.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.425][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:54.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.429][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-19 18:58:54.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-19 18:58:54.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.433][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:54.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.436][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.447][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-19 18:58:54.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-19 18:58:54.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-19 18:58:54.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-19 18:58:54.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:54.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:54.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.479][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:54.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:54.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.487][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:54.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-19 18:58:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-19 18:58:54.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-19 18:58:54.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.512][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-01-19 18:58:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.520][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.527][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:54.528][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:54.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-19 18:58:54.543][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-19 18:58:54.543][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-01-19 18:58:54.544][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-01-19 18:58:54.546][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.547][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.548][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:54.550][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.555][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:54.557][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:54.558][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:54.559][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:54.560][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:54.561][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:54.562][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-19 18:58:54.563][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.567][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.574][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.578][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.589][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:54.590][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:54.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-19 18:58:54.600][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.608][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.611][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.615][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.619][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.622][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.626][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-01-19 18:58:54.627][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:54.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.636][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[2025-01-19 18:58:54.640][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-19 18:58:54.641][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-01-19 18:58:54.642][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-01-19 18:58:54.643][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.645][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.646][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-19 18:58:54.647][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-19 18:58:54.648][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-19 18:58:54.649][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-19 18:58:54.654][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-19 18:58:54.655][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-19 18:58:54.657][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-19 18:58:54.658][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-19 18:58:54.659][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-19 18:58:54.660][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.664][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.668][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.671][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.675][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.682][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.686][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-01-19 18:58:54.687][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-01-19 18:58:54.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.696][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.TRACE[2025-01-19 18:58:54.697][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.701][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.704][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.708][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.712][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-19 18:58:54.719][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-19 18:58:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-19 18:58:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-19 18:58:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-19 18:58:54.722][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-19 18:58:54.723][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-19 18:58:54.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-19 18:58:54.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.733][FUN] Functions in observer BiodbConfig: [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 [2025-01-19 18:58:54.739][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-19 18:58:54.740][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-19 18:58:54.741][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-19 18:58:54.742][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-19 18:58:54.743][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-19 18:58:54.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-19 18:58:54.744][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-19 18:58:54.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-19 18:58:54.746][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-19 18:58:54.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
>
> proc.time()
user system elapsed
8.306 0.313 20.548