Multiple platform build/check report for BioC 3.21 - CHECK results for biodbHmdb on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
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*

CHECK results for biodbHmdb on nebbiolo1

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.

raw results

Summary

Package: biodbHmdb

Version: 1.13.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz

StartedAt: 2025-03-26 20:28:07 -0400 (Wed, 26 Mar 2025)

EndedAt: 2025-03-26 20:29:06 -0400 (Wed, 26 Mar 2025)

EllapsedTime: 59.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: biodbHmdb.Rcheck

Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... 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-3.21-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 ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL biodbHmdb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'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 [2025-03-26 20:28:38.645][biodb::testContext]
biodb.INFO [2025-03-26 20:28:38.647][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:38.648][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-03-26 20:28:38.649][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:38.650][biodb::testContext]
biodb.INFO [2025-03-26 20:28:38.651][biodb::testThat]
biodb.INFO [2025-03-26 20:28:38.652][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2025-03-26 20:28:38.653][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:38.654][biodb::testThat]
biodb.INFO [2025-03-26 20:28:38.739][biodb::testContext]
biodb.INFO [2025-03-26 20:28:38.740][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:38.741][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-26 20:28:38.742][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:38.743][biodb::testContext]
biodb.INFO [2025-03-26 20:28:38.750][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 20:28:38.752][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 20:28:38.758][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:38.759][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 20:28:38.760][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 20:28:38.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.764][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 20:28:38.788][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 20:28:38.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.791][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 20:28:38.792][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 20:28:38.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.796][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 20:28:38.797][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 20:28:38.798][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 20:28:38.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.801][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 20:28:38.802][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 20:28:38.803][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 20:28:38.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.807][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 20:28:38.808][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 20:28:38.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.811][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 20:28:38.812][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 20:28:38.813][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 20:28:38.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.817][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 20:28:38.818][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 20:28:38.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.821][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 20:28:38.822][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 20:28:38.828][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 20:28:38.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.833][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 20:28:38.834][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 20:28:38.835][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 20:28:38.836][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 20:28:38.837][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 20:28:38.839][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 20:28:38.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.843][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 20:28:38.844][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 20:28:38.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.848][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 20:28:38.849][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 20:28:38.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.853][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 20:28:38.854][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 20:28:38.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.858][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 20:28:38.859][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 20:28:38.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.863][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 20:28:38.864][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 20:28:38.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.868][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 20:28:38.869][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 20:28:38.873][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 20:28:38.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.877][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 20:28:38.878][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 20:28:38.879][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 20:28:38.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:38.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:38.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:38.886][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 20:28:38.926][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:38.945][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 20:28:38.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:38.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:38.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:38.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:38.953][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 20:28:38.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:38.955][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.956][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 20:28:38.957][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:38.958][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:38.959][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.960][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:38.960][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 20:28:38.960][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 20:28:38.960][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 20:28:38.960][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 20:28:38.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:38.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:38.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:38.965][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:38.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:38.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:38.980][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:38.981][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:38.982][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:38.983][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:38.984][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:38.985][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:38.986][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 20:28:38.988][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:38.989][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 20:28:38.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.991][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:38.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.993][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:38.994][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:38.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:38.996][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 20:28:38.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:38.998][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:38.999][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 20:28:39.000][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:39.001][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.002][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.004][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:39.004][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 20:28:39.004][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 20:28:39.004][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 20:28:39.004][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 20:28:39.005][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:39.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.008][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:39.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.011][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.012][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.013][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:39.014][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:39.015][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.016][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.017][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 20:28:39.019][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.020][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 20:28:39.021][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.022][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:39.023][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.027][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 20:28:39.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:39.030][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.031][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 20:28:39.032][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:39.033][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.034][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.035][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.036][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:39.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.038][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:39.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.042][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:39.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:39.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.046][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.047][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 20:28:39.048][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.049][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 20:28:39.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.051][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:39.052][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.053][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.054][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.056][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 20:28:39.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:39.058][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.059][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 20:28:39.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:39.061][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.062][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.063][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:39.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:39.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.070][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:39.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:39.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.074][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.078][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:39.078][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.161][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 20:28:39.165][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 20:28:39.167][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 20:28:39.168][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 20:28:39.169][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 20:28:39.171][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 20:28:39.172][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 20:28:39.173][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 20:28:39.175][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 20:28:39.176][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 20:28:39.177][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 20:28:39.178][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 20:28:39.180][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 20:28:39.181][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 20:28:39.182][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 20:28:39.184][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 20:28:39.185][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 20:28:39.186][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 20:28:39.188][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 20:28:39.189][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 20:28:39.190][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 20:28:39.192][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 20:28:39.193][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 20:28:39.194][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 20:28:39.196][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 20:28:39.197][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 20:28:39.198][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 20:28:39.200][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 20:28:39.201][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 20:28:39.202][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 20:28:39.204][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 20:28:39.205][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 20:28:39.206][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 20:28:39.208][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 20:28:39.209][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 20:28:39.210][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 20:28:39.211][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 20:28:39.213][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 20:28:39.214][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 20:28:39.215][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 20:28:39.217][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 20:28:39.218][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 20:28:39.219][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 20:28:39.221][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 20:28:39.222][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 20:28:39.224][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 20:28:39.225][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 20:28:39.226][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 20:28:39.228][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 20:28:39.229][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 20:28:39.230][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 20:28:39.232][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 20:28:39.233][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 20:28:39.234][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 20:28:39.236][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 20:28:39.237][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 20:28:39.238][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 20:28:39.240][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 20:28:39.241][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 20:28:39.242][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 20:28:39.244][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 20:28:39.245][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 20:28:39.246][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 20:28:39.248][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 20:28:39.249][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 20:28:39.250][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 20:28:39.252][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 20:28:39.253][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 20:28:39.254][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 20:28:39.256][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 20:28:39.257][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 20:28:39.258][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 20:28:39.260][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 20:28:39.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 20:28:39.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 20:28:39.264][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 20:28:39.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 20:28:39.266][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 20:28:39.268][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 20:28:39.269][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 20:28:39.270][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 20:28:39.272][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 20:28:39.273][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 20:28:39.279][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 20:28:39.280][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 20:28:39.283][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:39.284][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.286][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.394][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[2025-03-26 20:28:39.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.400][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[2025-03-26 20:28:39.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.406][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[2025-03-26 20:28:39.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:39.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:39.426][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-26 20:28:39.436][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:39.439][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.440][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:39.443][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.444][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-26 20:28:39.445][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.447][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 20:28:39.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:39.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.450][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-26 20:28:39.451][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-26 20:28:39.452][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-26 20:28:39.453][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:39.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:39.454][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-26 20:28:39.454][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-26 20:28:39.455][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 20:28:39.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.458][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:39.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:39.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:39.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:39.461][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-26 20:28:39.461][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-26 20:28:39.462][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:39.463][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:39.464][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:39.465][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:39.471][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-26 20:28:39.473][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 20:28:39.474][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 20:28:39.476][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 20:28:39.477][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 20:28:39.499][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:39.500][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-26 20:28:39.504][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:39.508][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:39.512][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:39.513][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:39.515][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-26 20:28:39.515][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-26 20:28:39.517][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-26 20:28:39.517][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-26 20:28:39.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:39.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:39.519][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-26 20:28:39.520][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-26 20:28:39.521][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:39.544][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:39.546][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:39.547][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:39.548][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:39.549][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:39.550][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-26 20:28:39.558][biodb::testThat]
biodb.INFO [2025-03-26 20:28:39.559][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-26 20:28:39.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:39.561][biodb::testThat]
biodb.TRACE[2025-03-26 20:28:39.565][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-03-26 20:28:39.566][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:39.570][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:39.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:39.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:39.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:39.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:39.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:39.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:39.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:39.597][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:39.599][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:39.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.601][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:39.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:39.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.618][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:39.619][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:39.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.621][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.647][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:39.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.651][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.653][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.660][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.661][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.663][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.664][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.669][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.670][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.672][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.677][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.678][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.686][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.687][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.700][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.704][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:39.705][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:39.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.707][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:39.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:39.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.713][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.714][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.721][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.722][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.729][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:39.730][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:39.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.732][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:39.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:39.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.737][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:39.738][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:39.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:39.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:39.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.746][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.747][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.754][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.755][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.757][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.762][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:39.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:39.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.765][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:39.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:39.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.770][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:39.771][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:39.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:39.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:39.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.779][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:39.780][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:39.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.783][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:39.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:39.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.787][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:39.788][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.791][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:39.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:39.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:39.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:39.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:39.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:39.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:39.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.841][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.845][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.853][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.857][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.861][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:39.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:39.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:39.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.895][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:39.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.903][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.906][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:39.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.914][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.918][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:39.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.922][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:39.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:39.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.926][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:39.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.929][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:39.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:39.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:39.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:39.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:39.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:39.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:39.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:39.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:39.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:39.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:39.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:39.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:39.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:39.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.968][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.972][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.979][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:39.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:39.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:39.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:39.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:39.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:39.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:39.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.006][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.014][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.018][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.021][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.025][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.037][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.041][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:40.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:40.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.101][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.109][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:40.140][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-26 20:28:40.142][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 20:28:40.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 20:28:40.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 20:28:40.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 20:28:40.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 20:28:40.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 20:28:40.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 20:28:40.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 20:28:40.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.181][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.214][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.217][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.221][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:40.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.243][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.244][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.262][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.266][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.270][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.274][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.275][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.278][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.300][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.301][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.315][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.319][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.326][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.327][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.367][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.375][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.379][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.380][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.383][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.409][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.410][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.424][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:40.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:40.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.428][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:40.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:40.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.432][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:40.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:40.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.435][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:40.436][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:40.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.439][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:40.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:40.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:40.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:40.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.454][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:40.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:40.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:40.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:40.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.462][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:40.463][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:40.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.465][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:40.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:40.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.476][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.484][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.488][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.489][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.491][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.492][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.514][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.515][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.517][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.544][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.545][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.570][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.571][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.597][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.598][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.600][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.615][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:40.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:40.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:40.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:40.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:40.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:40.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.649][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:40.650][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:40.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:40.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:40.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.679][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.680][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.682][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.694][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.698][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.701][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.705][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.706][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.709][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.720][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.721][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.723][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.727][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.728][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.730][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.734][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.735][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.737][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.742][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.748][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.749][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.755][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.756][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:40.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.763][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.764][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:40.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.765][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.770][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.771][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:40.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.772][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.776][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:40.777][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:40.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.783][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:40.785][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:40.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.791][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:40.792][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:40.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.798][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.799][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:40.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.800][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.805][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.806][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.813][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:40.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.820][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.824][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:40.825][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:40.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.831][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.832][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.834][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.839][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.840][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.846][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:40.847][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:40.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.849][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 20:28:40.856][biodb::testThat]
biodb.INFO [2025-03-26 20:28:40.858][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-26 20:28:40.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:40.859][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:40.874][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-26 20:28:40.881][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-26 20:28:40.886][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:40.887][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-26 20:28:40.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-26 20:28:40.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 20:28:40.893][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-26 20:28:40.894][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 20:28:40.918][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:40.919][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:40.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:40.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:40.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:40.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:40.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:40.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:40.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:40.934][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.935][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:40.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:40.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.942][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.943][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:40.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.950][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.951][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:40.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.964][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.965][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.968][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:40.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.973][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:40.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.980][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.981][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:40.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.988][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.989][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:40.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:40.996][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.997][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:40.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:40.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.000][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.004][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.005][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.007][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.012][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.013][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.015][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.020][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:41.021][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:41.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:41.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:41.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.028][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:41.029][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:41.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.031][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:41.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.036][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.037][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.044][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.045][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.047][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.052][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.053][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.060][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.061][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.064][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.068][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:41.069][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:41.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.073][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:41.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:41.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.077][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:41.078][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.081][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:41.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.100][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:41.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.104][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:41.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:41.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.108][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.112][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:41.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:41.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.116][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:41.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:41.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.119][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:41.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:41.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:41.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:41.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:41.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:41.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:41.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:41.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:41.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:41.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:41.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:41.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:41.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.146][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.166][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:41.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.177][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:41.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.181][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.185][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.193][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:41.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.197][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:41.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:41.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.200][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:41.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:41.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:41.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:41.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.227][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:41.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:41.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.235][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:41.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:41.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:41.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.277][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.281][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.285][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.289][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:41.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:41.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.293][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:41.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:41.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.300][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:41.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.316][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:41.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.340][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:41.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:41.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.344][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.352][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:41.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:41.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:41.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:41.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.384][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-26 20:28:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-26 20:28:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-26 20:28:41.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-26 20:28:41.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-26 20:28:41.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-26 20:28:41.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-26 20:28:41.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 20:28:41.403][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.404][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-26 20:28:41.405][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:41.405][biodb::testThat]
biodb.TRACE[2025-03-26 20:28:41.408][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.411][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.413][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-03-26 20:28:41.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.451][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-03-26 20:28:41.453][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-26 20:28:41.454][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-26 20:28:41.455][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-26 20:28:41.456][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.458][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.459][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:41.460][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.461][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:41.462][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:41.463][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:41.465][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:41.466][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:41.467][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:41.467][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-26 20:28:41.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.481][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.485][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:41.486][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:41.487][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-26 20:28:41.497][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.503][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.505][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.506][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-03-26 20:28:41.517][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.521][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.525][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.531][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-03-26 20:28:41.582][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-26 20:28:41.584][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-26 20:28:41.585][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-26 20:28:41.599][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.601][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.602][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:41.604][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.605][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:41.625][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:41.626][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:41.627][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:41.628][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:41.629][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:41.630][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-26 20:28:41.631][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.639][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.643][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:41.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:41.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.647][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:41.648][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:41.649][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-26 20:28:41.659][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.660][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.662][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.664][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-03-26 20:28:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.678][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.682][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.688][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-03-26 20:28:41.689][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-03-26 20:28:41.690][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-26 20:28:41.691][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-26 20:28:41.693][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.694][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.695][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:41.697][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.698][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:41.699][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:41.700][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:41.701][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:41.702][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:41.703][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:41.704][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-26 20:28:41.705][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.709][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.713][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.717][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:41.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.721][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:41.722][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:41.723][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-03-26 20:28:41.736][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.737][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-26 20:28:41.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:41.739][biodb::testThat]
biodb.TRACE[2025-03-26 20:28:41.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.774][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-26 20:28:41.775][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-26 20:28:41.776][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-26 20:28:41.777][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.779][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.780][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:41.782][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:41.782][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:41.784][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:41.785][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:41.786][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:41.787][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:41.788][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:41.789][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-26 20:28:41.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:41.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:41.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:41.806][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:41.807][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-03-26 20:28:41.820][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.821][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-26 20:28:41.822][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:41.823][biodb::testThat]
biodb.TRACE[2025-03-26 20:28:41.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 20:28:41.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 20:28:41.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 20:28:41.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 20:28:41.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 20:28:41.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 20:28:41.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 20:28:41.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:41.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 20:28:41.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 20:28:41.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:41.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 20:28:41.925][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.926][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-26 20:28:41.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:41.927][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.935][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.936][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-26 20:28:41.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:41.938][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.945][biodb::testThat]
biodb.INFO [2025-03-26 20:28:41.946][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-26 20:28:41.947][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:41.947][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:41.951][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-03-26 20:28:51.654][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-03-26 20:28:51.717][biodb::testThat]
biodb.INFO [2025-03-26 20:28:51.719][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-26 20:28:51.721][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:51.722][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:54.838][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-03-26 20:28:54.893][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:54.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:54.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:54.904][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:54.906][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:54.909][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:54.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:54.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:54.917][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:54.919][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:54.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:54.923][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 20:28:54.926][biodb::testThat]
biodb.INFO [2025-03-26 20:28:54.928][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-26 20:28:54.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:54.931][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:54.935][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-26 20:28:55.009][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-26 20:28:55.011][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.013][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-26 20:28:55.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-26 20:28:55.032][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 20:28:55.033][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 20:28:55.034][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 20:28:55.035][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.037][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:55.038][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:55.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:55.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:55.051][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.055][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:55.113][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-26 20:28:55.113][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-26 20:28:55.129][biodb::testThat]
biodb.INFO [2025-03-26 20:28:55.130][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-26 20:28:55.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:55.132][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:55.139][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-03-26 20:28:55.140][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-03-26 20:28:55.141][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-03-26 20:28:55.143][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-03-26 20:28:55.144][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-03-26 20:28:55.145][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-03-26 20:28:55.146][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-03-26 20:28:55.148][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-03-26 20:28:55.149][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-26 20:28:55.151][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-26 20:28:55.152][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-26 20:28:55.153][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-03-26 20:28:55.155][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker3362603601c78dmarker".
biodb.TRACE[2025-03-26 20:28:55.157][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-03-26 20:28:55.158][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-26 20:28:55.159][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-26 20:28:55.161][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-03-26 20:28:55.162][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2025-03-26 20:28:55.163][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-26 20:28:55.164][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2025-03-26 20:28:55.171][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2025-03-26 20:28:55.172][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-03-26 20:28:55.173][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-03-26 20:28:55.174][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2025-03-26 20:28:55.182][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2025-03-26 20:28:55.183][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-26 20:28:55.185][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-26 20:28:55.186][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-03-26 20:28:55.188][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker3362605fac013emarker".
biodb.TRACE[2025-03-26 20:28:55.189][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-03-26 20:28:55.190][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-03-26 20:28:55.191][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-03-26 20:28:55.193][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 20:28:55.194][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 20:28:55.195][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 20:28:55.196][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.197][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:55.198][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:55.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:55.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:55.211][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:55.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:55.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:55.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:55.248][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-26 20:28:55.248][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-26 20:28:55.249][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-03-26 20:28:55.262][biodb::testThat]
biodb.INFO [2025-03-26 20:28:55.263][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-26 20:28:55.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:55.265][biodb::testThat]
biodb.INFO [2025-03-26 20:28:55.286][biodb::testThat]
biodb.INFO [2025-03-26 20:28:55.287][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-26 20:28:55.288][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:55.289][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:55.291][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.293][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.294][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:55.296][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.297][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:55.298][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:55.299][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:55.300][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:55.301][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-03-26 20:28:55.308][biodb::testThat]
biodb.INFO [2025-03-26 20:28:55.309][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-26 20:28:55.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:55.311][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:55.314][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.315][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.316][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:55.318][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:55.319][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:55.320][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:55.321][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:55.322][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:55.323][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-03-26 20:28:55.336][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:55.337][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:55.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.340][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:55.341][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:55.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:55.344][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:55.345][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:55.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:55.347][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 20:28:55.348][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 20:28:55.349][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-26 20:28:55.356][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-26 20:28:55.357][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 20:28:55.358][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.360][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.362][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 20:28:55.366][biodb::testContext]
biodb.INFO [2025-03-26 20:28:55.367][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:55.368][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-03-26 20:28:55.369][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:55.370][biodb::testContext]
biodb.INFO [2025-03-26 20:28:55.374][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 20:28:55.376][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 20:28:55.379][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:55.380][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 20:28:55.381][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 20:28:55.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.385][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 20:28:55.386][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 20:28:55.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.389][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[2025-03-26 20:28:55.389][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 20:28:55.391][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 20:28:55.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.394][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 20:28:55.395][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 20:28:55.396][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 20:28:55.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.400][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 20:28:55.401][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 20:28:55.402][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 20:28:55.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.406][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 20:28:55.407][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 20:28:55.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.411][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 20:28:55.412][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 20:28:55.413][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 20:28:55.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.417][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 20:28:55.418][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 20:28:55.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.421][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 20:28:55.422][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 20:28:55.424][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 20:28:55.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.427][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 20:28:55.428][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 20:28:55.429][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 20:28:55.430][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 20:28:55.431][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 20:28:55.432][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 20:28:55.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.436][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 20:28:55.437][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 20:28:55.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.441][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 20:28:55.446][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 20:28:55.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.449][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[2025-03-26 20:28:55.450][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 20:28:55.451][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 20:28:55.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.455][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 20:28:55.456][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 20:28:55.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.458][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[2025-03-26 20:28:55.459][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 20:28:55.460][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 20:28:55.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.464][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 20:28:55.465][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 20:28:55.469][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 20:28:55.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.473][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 20:28:55.474][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 20:28:55.475][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 20:28:55.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.479][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 20:28:55.481][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.482][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 20:28:55.483][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.484][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:55.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.489][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 20:28:55.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:55.491][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.492][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 20:28:55.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:55.494][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.496][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:55.496][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 20:28:55.496][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 20:28:55.496][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 20:28:55.496][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 20:28:55.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:55.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:55.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.504][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:55.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:55.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.508][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.509][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 20:28:55.511][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.512][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 20:28:55.513][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.514][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:55.515][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.517][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.520][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 20:28:55.521][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:55.522][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.523][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 20:28:55.524][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:55.525][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.526][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.527][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:55.527][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 20:28:55.527][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 20:28:55.527][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 20:28:55.527][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 20:28:55.528][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:55.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.531][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:55.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.534][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.535][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:55.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:55.538][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.539][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.540][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 20:28:55.542][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.543][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 20:28:55.544][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.545][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:55.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.548][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.549][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.550][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 20:28:55.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:55.552][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.553][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 20:28:55.554][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:55.555][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.561][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.562][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.563][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:55.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:55.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.568][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.569][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.570][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:55.571][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:55.572][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.573][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.574][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 20:28:55.576][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.577][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 20:28:55.578][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:55.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.584][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 20:28:55.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:55.586][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.586][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 20:28:55.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:55.588][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.590][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:55.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:55.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.598][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:55.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:55.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.602][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:55.603][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:55.604][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.647][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[2025-03-26 20:28:55.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.721][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 20:28:55.723][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 20:28:55.724][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 20:28:55.726][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 20:28:55.727][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 20:28:55.729][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 20:28:55.730][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 20:28:55.732][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 20:28:55.733][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 20:28:55.735][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 20:28:55.736][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 20:28:55.738][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 20:28:55.739][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 20:28:55.741][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 20:28:55.742][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 20:28:55.744][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 20:28:55.745][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 20:28:55.747][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 20:28:55.748][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 20:28:55.750][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 20:28:55.751][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 20:28:55.753][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 20:28:55.754][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 20:28:55.756][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 20:28:55.757][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 20:28:55.759][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 20:28:55.761][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 20:28:55.763][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 20:28:55.764][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 20:28:55.766][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 20:28:55.768][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 20:28:55.770][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 20:28:55.771][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 20:28:55.773][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 20:28:55.775][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 20:28:55.776][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 20:28:55.778][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 20:28:55.780][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 20:28:55.782][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 20:28:55.783][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 20:28:55.785][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 20:28:55.786][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 20:28:55.788][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 20:28:55.789][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 20:28:55.791][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 20:28:55.792][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 20:28:55.794][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 20:28:55.796][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 20:28:55.797][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 20:28:55.799][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 20:28:55.800][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 20:28:55.802][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 20:28:55.804][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 20:28:55.805][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 20:28:55.807][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 20:28:55.808][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 20:28:55.810][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 20:28:55.811][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 20:28:55.813][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 20:28:55.819][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 20:28:55.820][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 20:28:55.822][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 20:28:55.823][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 20:28:55.824][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 20:28:55.826][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 20:28:55.827][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 20:28:55.828][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 20:28:55.830][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 20:28:55.831][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 20:28:55.832][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 20:28:55.834][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 20:28:55.835][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 20:28:55.836][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 20:28:55.838][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 20:28:55.839][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 20:28:55.840][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 20:28:55.842][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 20:28:55.843][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 20:28:55.844][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 20:28:55.846][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 20:28:55.847][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 20:28:55.848][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 20:28:55.850][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 20:28:55.851][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 20:28:55.853][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 20:28:55.854][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:55.855][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.856][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.937][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[2025-03-26 20:28:55.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:55.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:55.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:55.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:55.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:55.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:55.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:55.970][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-26 20:28:55.971][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:55.973][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.974][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.975][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.976][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:55.977][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.978][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-26 20:28:55.979][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.980][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.981][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 20:28:55.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:55.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:55.984][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-26 20:28:55.985][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-26 20:28:55.986][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-26 20:28:55.987][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:55.988][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:55.988][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-26 20:28:55.988][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-26 20:28:55.989][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 20:28:55.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:55.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:55.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:55.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:55.996][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-26 20:28:55.996][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-26 20:28:55.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:55.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:55.999][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.000][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.001][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-26 20:28:56.003][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 20:28:56.004][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 20:28:56.006][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 20:28:56.007][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 20:28:56.011][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:56.012][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-26 20:28:56.013][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:56.015][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:56.016][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:56.017][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:56.018][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-26 20:28:56.019][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-26 20:28:56.020][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-26 20:28:56.020][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-26 20:28:56.021][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:56.022][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:56.023][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-26 20:28:56.024][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-26 20:28:56.025][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:56.026][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:56.032][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:56.033][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:56.035][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:56.036][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:56.037][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-26 20:28:56.038][biodb::testThat]
biodb.INFO [2025-03-26 20:28:56.039][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-03-26 20:28:56.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:56.041][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:56.045][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:56.047][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:56.048][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:56.049][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:56.050][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:56.051][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:56.052][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:56.053][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:56.054][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:56.057][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-26 20:28:56.063][biodb::testThat]
biodb.INFO [2025-03-26 20:28:56.064][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-03-26 20:28:56.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:56.066][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:56.067][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-26 20:28:56.068][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-26 20:28:56.070][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:56.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-26 20:28:56.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-26 20:28:56.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 20:28:56.076][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-26 20:28:56.077][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 20:28:56.078][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:56.080][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:56.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:56.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:56.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:56.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.090][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.TRACE[2025-03-26 20:28:56.094][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.102][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.103][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.106][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.110][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.111][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.119][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.120][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.127][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.136][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.137][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.150][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.151][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.153][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.154][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.158][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.159][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.167][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.168][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.175][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.176][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.178][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.180][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.184][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:56.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:56.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:56.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.192][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:56.193][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:56.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.200][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.201][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.216][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.217][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.224][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:56.225][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:56.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:56.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.232][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:56.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:56.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.237][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:56.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:56.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.241][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:56.242][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.245][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:56.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.272][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.276][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.280][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.284][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:56.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:56.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:56.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.315][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:56.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.323][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:56.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.338][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:56.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.346][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:56.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.350][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:56.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:56.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.354][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:56.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:56.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:56.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.366][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:56.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:56.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:56.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:56.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:56.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:56.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:56.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.397][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.405][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:56.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:56.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.437][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.441][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:56.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.445][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.448][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.452][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:56.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.456][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:56.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:56.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:56.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:56.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:56.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:56.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.473][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:56.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.488][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:56.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:56.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:56.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:56.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.519][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:56.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:56.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:56.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:56.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:56.557][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-26 20:28:56.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:56.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 20:28:56.584][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 20:28:56.585][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-26 20:28:56.586][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-26 20:28:56.587][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 20:28:56.588][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:56.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:56.591][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.593][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 20:28:56.600][biodb::testContext]
biodb.INFO [2025-03-26 20:28:56.601][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:56.601][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-03-26 20:28:56.602][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 20:28:56.604][biodb::testContext]
biodb.INFO [2025-03-26 20:28:56.608][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 20:28:56.610][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 20:28:56.615][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:56.616][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 20:28:56.617][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 20:28:56.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.621][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 20:28:56.622][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 20:28:56.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.626][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 20:28:56.627][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 20:28:56.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.631][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 20:28:56.632][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 20:28:56.633][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 20:28:56.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.636][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 20:28:56.637][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 20:28:56.638][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 20:28:56.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.642][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 20:28:56.643][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 20:28:56.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.647][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 20:28:56.648][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 20:28:56.649][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 20:28:56.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.652][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 20:28:56.653][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 20:28:56.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.657][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 20:28:56.658][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 20:28:56.659][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 20:28:56.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.663][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 20:28:56.664][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 20:28:56.665][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 20:28:56.666][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 20:28:56.667][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 20:28:56.668][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 20:28:56.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.671][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 20:28:56.672][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 20:28:56.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.676][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 20:28:56.677][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 20:28:56.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.681][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 20:28:56.682][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 20:28:56.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.685][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 20:28:56.687][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 20:28:56.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.690][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 20:28:56.696][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 20:28:56.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.700][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 20:28:56.701][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 20:28:56.705][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 20:28:56.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.708][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 20:28:56.709][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 20:28:56.710][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 20:28:56.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.714][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 20:28:56.716][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.717][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 20:28:56.718][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.719][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:56.720][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.721][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.722][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.723][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.724][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 20:28:56.725][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:56.726][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.727][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 20:28:56.728][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:56.729][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.730][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.731][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:56.731][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 20:28:56.731][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 20:28:56.731][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 20:28:56.731][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 20:28:56.732][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:56.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.734][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:56.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.738][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.739][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:56.740][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:56.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.742][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.743][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 20:28:56.745][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.746][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 20:28:56.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:56.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.751][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.752][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.753][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 20:28:56.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:56.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.756][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 20:28:56.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:56.758][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.759][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:56.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 20:28:56.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 20:28:56.760][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 20:28:56.760][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 20:28:56.761][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:56.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:56.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.768][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.768][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:56.769][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:56.770][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.771][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.773][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 20:28:56.774][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.775][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 20:28:56.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:56.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.779][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.780][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.782][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 20:28:56.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:56.784][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.785][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 20:28:56.786][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:56.787][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.788][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.789][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.790][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:56.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.793][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:56.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.797][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:56.803][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:56.804][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.805][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.807][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 20:28:56.808][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.809][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 20:28:56.810][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.811][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:56.812][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.813][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.816][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 20:28:56.817][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:56.818][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.819][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 20:28:56.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:56.821][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:56.823][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.824][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 20:28:56.825][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:56.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:56.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:56.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:56.830][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:56.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:56.833][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:56.834][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:56.835][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:56.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.855][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[2025-03-26 20:28:56.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:56.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:56.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:56.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:56.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:56.918][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 20:28:56.920][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 20:28:56.921][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 20:28:56.923][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 20:28:56.924][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 20:28:56.925][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 20:28:56.927][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 20:28:56.928][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 20:28:56.930][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 20:28:56.931][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 20:28:56.932][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 20:28:56.934][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 20:28:56.935][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 20:28:56.936][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 20:28:56.938][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 20:28:56.939][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 20:28:56.940][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 20:28:56.942][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 20:28:56.943][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 20:28:56.944][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 20:28:56.946][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 20:28:56.947][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 20:28:56.949][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 20:28:56.950][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 20:28:56.951][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 20:28:56.953][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 20:28:56.954][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 20:28:56.955][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 20:28:56.957][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 20:28:56.958][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 20:28:56.960][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 20:28:56.961][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 20:28:56.962][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 20:28:56.964][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 20:28:56.965][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 20:28:56.966][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 20:28:56.968][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 20:28:56.969][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 20:28:56.970][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 20:28:56.972][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 20:28:56.973][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 20:28:56.974][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 20:28:56.976][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 20:28:56.977][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 20:28:56.979][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 20:28:56.980][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 20:28:56.981][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 20:28:56.983][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 20:28:56.984][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 20:28:56.985][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 20:28:56.987][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 20:28:56.988][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 20:28:56.990][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 20:28:56.991][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 20:28:56.992][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 20:28:56.994][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 20:28:56.995][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 20:28:56.996][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 20:28:56.998][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 20:28:56.999][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 20:28:57.001][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 20:28:57.007][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 20:28:57.008][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 20:28:57.010][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 20:28:57.011][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 20:28:57.012][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 20:28:57.014][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 20:28:57.015][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 20:28:57.016][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 20:28:57.018][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 20:28:57.019][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 20:28:57.020][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 20:28:57.022][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 20:28:57.023][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 20:28:57.024][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 20:28:57.026][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 20:28:57.027][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 20:28:57.028][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 20:28:57.030][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 20:28:57.031][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 20:28:57.032][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 20:28:57.034][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 20:28:57.035][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 20:28:57.037][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 20:28:57.038][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 20:28:57.039][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 20:28:57.040][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.042][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.086][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[2025-03-26 20:28:57.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.115][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[2025-03-26 20:28:57.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 20:28:57.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.153][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-26 20:28:57.154][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:57.156][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:57.157][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 20:28:57.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:57.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 20:28:57.160][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:57.161][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-26 20:28:57.162][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:57.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 20:28:57.164][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 20:28:57.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 20:28:57.166][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:57.167][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-26 20:28:57.168][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-26 20:28:57.169][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-26 20:28:57.170][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 20:28:57.171][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 20:28:57.171][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-26 20:28:57.171][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-26 20:28:57.172][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 20:28:57.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:57.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:57.175][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 20:28:57.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 20:28:57.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 20:28:57.178][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 20:28:57.179][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-26 20:28:57.179][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-26 20:28:57.180][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:57.181][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:57.182][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 20:28:57.183][self$setPropertyValue]
biodb.DEBUG[2025-03-26 20:28:57.184][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-26 20:28:57.186][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 20:28:57.187][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 20:28:57.189][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 20:28:57.190][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 20:28:57.193][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:57.194][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-26 20:28:57.195][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:57.197][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:57.198][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:57.199][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:57.200][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-26 20:28:57.201][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-26 20:28:57.202][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-26 20:28:57.202][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-26 20:28:57.203][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 20:28:57.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 20:28:57.210][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-26 20:28:57.211][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-26 20:28:57.212][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-26 20:28:57.214][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:57.215][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:57.216][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:57.217][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-26 20:28:57.218][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 20:28:57.219][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-26 20:28:57.221][biodb::testThat]
biodb.INFO [2025-03-26 20:28:57.221][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2025-03-26 20:28:57.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 20:28:57.223][biodb::testThat]
biodb.DEBUG[2025-03-26 20:28:57.225][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-26 20:28:57.226][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-03-26 20:28:57.227][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-03-26 20:28:57.230][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:57.232][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:57.233][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:57.234][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:57.235][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:57.237][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:57.238][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:57.239][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:57.240][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:57.240][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:57.241][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-03-26 20:28:57.243][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-26 20:28:57.244][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-26 20:28:57.246][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:57.247][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-26 20:28:57.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-26 20:28:57.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 20:28:57.252][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-26 20:28:57.253][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 20:28:57.254][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:57.255][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:57.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:57.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:57.270][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.278][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.279][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.282][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.286][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.288][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.289][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.295][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.296][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.299][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.304][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.312][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.313][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.326][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.327][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.330][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.334][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.335][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.343][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.344][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.352][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.353][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.360][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.361][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.363][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.368][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.369][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.371][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.377][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.378][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.385][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.386][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.393][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.402][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.403][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.406][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.410][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:57.411][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:57.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.415][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:57.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:57.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.419][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:57.420][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.434][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:57.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.451][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.455][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.459][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.463][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.466][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.470][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.533][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.547][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.586][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.590][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.594][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:57.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.622][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.625][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.634][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.637][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.641][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:57.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:57.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.659][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:57.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:57.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.663][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:57.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.679][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:57.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:57.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:57.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.704][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:57.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:57.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.708][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:57.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:57.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.715][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:57.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:57.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:57.743][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-26 20:28:57.744][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.748][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.758][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:57.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:57.772][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:57.773][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:57.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:57.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:57.790][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-26 20:28:57.791][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-03-26 20:28:57.793][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-03-26 20:28:57.795][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-03-26 20:28:57.796][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-03-26 20:28:57.797][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-03-26 20:28:57.800][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-03-26 20:28:57.801][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-26 20:28:57.802][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-26 20:28:57.804][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-26 20:28:57.805][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-03-26 20:28:57.807][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker336260107a0f8fmarker".
biodb.TRACE[2025-03-26 20:28:57.809][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-03-26 20:28:57.810][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-26 20:28:57.811][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-26 20:28:57.813][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-03-26 20:28:57.814][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2025-03-26 20:28:57.816][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-26 20:28:57.817][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2025-03-26 20:28:57.820][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2025-03-26 20:28:57.821][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-03-26 20:28:57.822][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-03-26 20:28:57.824][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2025-03-26 20:28:57.832][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2025-03-26 20:28:57.833][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-26 20:28:57.835][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-26 20:28:57.836][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-03-26 20:28:57.838][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker3362606ee69f9fmarker".
biodb.TRACE[2025-03-26 20:28:57.839][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-03-26 20:28:57.840][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-03-26 20:28:57.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-26 20:28:57.843][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 20:28:57.845][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-26 20:28:57.847][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 20:28:57.848][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-26 20:28:57.850][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-26 20:28:57.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:57.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:57.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:57.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:57.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:57.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:57.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:57.868][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.869][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.871][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:57.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:57.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.878][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.879][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.882][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:57.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.887][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.888][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.892][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:57.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.897][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.898][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.900][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.914][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:57.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.920][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.921][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:57.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.930][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.931][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:57.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.938][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.939][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.941][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.943][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:57.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.947][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.948][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.950][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.952][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:57.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.956][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.957][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.960][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:57.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.964][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.966][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.968][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:57.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.973][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.974][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.976][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:57.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:57.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.982][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.983][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.985][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:57.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:57.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.990][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.991][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.993][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:57.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:57.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:57.998][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.000][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.001][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.007][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.008][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.015][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.016][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.018][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.019][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.023][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:58.029][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:58.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.031][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:58.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:58.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.037][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:58.038][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.041][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-26 20:28:58.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.057][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:58.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:58.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.061][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:58.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:58.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.065][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 20:28:58.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 20:28:58.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.069][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:58.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:58.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.073][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:58.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:58.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.077][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-26 20:28:58.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-26 20:28:58.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:58.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:58.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:58.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:58.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 20:28:58.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 20:28:58.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:58.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:58.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:58.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:58.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:58.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-26 20:28:58.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.106][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:58.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:58.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:58.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:58.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:58.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-26 20:28:58.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.118][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:58.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:58.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:58.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:58.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:58.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-26 20:28:58.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.130][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.144][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-26 20:28:58.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.149][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.152][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.156][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:58.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:58.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:58.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:58.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.168][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 20:28:58.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 20:28:58.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:58.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:58.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:58.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 20:28:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 20:28:58.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:58.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:58.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.200][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:58.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:58.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.203][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 20:28:58.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 20:28:58.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:58.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:58.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.235][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:58.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:58.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:58.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-26 20:28:58.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.247][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:58.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:58.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.251][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:58.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:58.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.255][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:58.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-26 20:28:58.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:58.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 20:28:58.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 20:28:58.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.270][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:58.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-26 20:28:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 20:28:58.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 20:28:58.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 20:28:58.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.311][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:58.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:58.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.314][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:58.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:58.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.322][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:58.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-26 20:28:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 20:28:58.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 20:28:58.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:58.356][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-26 20:28:58.357][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.361][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.365][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:58.373][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:58.374][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:58.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:58.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:58.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:58.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:58.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:58.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:58.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 20:28:58.390][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-26 20:28:58.391][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-26 20:28:58.392][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-26 20:28:58.393][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:58.395][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:58.396][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:58.398][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:58.399][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:58.400][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:58.401][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:58.402][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:58.403][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:58.404][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:58.405][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-26 20:28:58.407][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.411][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.415][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.419][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.423][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.427][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.431][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:58.435][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:58.436][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:58.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:58.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:58.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:58.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:58.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:58.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:58.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:58.447][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.451][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.455][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.464][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.469][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.473][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.477][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:58.481][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-26 20:28:58.481][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:58.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:58.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:58.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:58.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:58.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:58.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:58.491][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[2025-03-26 20:28:58.496][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-26 20:28:58.497][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-26 20:28:58.498][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-26 20:28:58.500][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:58.501][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:58.503][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-26 20:28:58.504][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-26 20:28:58.505][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-26 20:28:58.506][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-26 20:28:58.507][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-26 20:28:58.508][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-26 20:28:58.509][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-26 20:28:58.510][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-26 20:28:58.511][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-26 20:28:58.513][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.517][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.521][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.529][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.533][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:58.541][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-26 20:28:58.542][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-03-26 20:28:58.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:58.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:58.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:58.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:58.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:58.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:58.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 20:28:58.553][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.557][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.561][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.569][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.574][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.578][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 20:28:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-26 20:28:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-26 20:28:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 20:28:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 20:28:58.586][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-26 20:28:58.587][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-26 20:28:58.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 20:28:58.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:58.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:58.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:58.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:58.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:58.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 20:28:58.604][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 20:28:58.605][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-26 20:28:58.606][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-26 20:28:58.607][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 20:28:58.608][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 20:28:58.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 20:28:58.610][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 20:28:58.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 20:28:58.611][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 20:28:58.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
  8.722   0.469  21.849

CHECK results for biodbHmdb on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings