Multiple platform build/check report for BioC 3.20 - CHECK results for biodbHmdb on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for biodbHmdb on teran2

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: 1.12.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbHmdb_1.12.0.tar.gz

StartedAt: 2024-11-19 23:30:22 -0500 (Tue, 19 Nov 2024)

EndedAt: 2024-11-19 23:31:01 -0500 (Tue, 19 Nov 2024)

EllapsedTime: 39.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: biodbHmdb.Rcheck

Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbHmdb_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbHmdb
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-11-19 23:30:47.409][biodb::testContext]
biodb.INFO [2024-11-19 23:30:47.410][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:47.411][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2024-11-19 23:30:47.412][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:47.412][biodb::testContext]
biodb.INFO [2024-11-19 23:30:47.413][biodb::testThat]
biodb.INFO [2024-11-19 23:30:47.414][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2024-11-19 23:30:47.415][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:47.415][biodb::testThat]
biodb.INFO [2024-11-19 23:30:47.485][biodb::testContext]
biodb.INFO [2024-11-19 23:30:47.485][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:47.486][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-19 23:30:47.487][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:47.487][biodb::testContext]
biodb.INFO [2024-11-19 23:30:47.493][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:47.494][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:47.505][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:47.506][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:30:47.507][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:30:47.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.509][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:30:47.523][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:30:47.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.526][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:30:47.527][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:30:47.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.529][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:30:47.530][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:30:47.531][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:30:47.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.533][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:30:47.534][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:30:47.535][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:30:47.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.537][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:30:47.538][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:30:47.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.540][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:30:47.541][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:30:47.542][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:30:47.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.544][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:30:47.545][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:30:47.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.547][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:30:47.548][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:30:47.549][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:30:47.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.551][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:47.552][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:30:47.553][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:30:47.553][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:30:47.554][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:30:47.555][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:30:47.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.557][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:30:47.558][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:30:47.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.561][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:30:47.561][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:30:47.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.564][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:30:47.565][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:30:47.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.567][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:30:47.568][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:30:47.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.570][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:30:47.571][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:30:47.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.574][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:47.574][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:30:47.577][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:30:47.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.580][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:30:47.581][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:30:47.581][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:30:47.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.586][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:30:47.609][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.620][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 23:30:47.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:47.623][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.632][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:47.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:47.633][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.634][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:30:47.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:47.635][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.636][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.637][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:47.637][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:47.637][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:47.637][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:47.637][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:47.637][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:47.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:47.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.642][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:47.643][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:47.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.645][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.646][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:30:47.647][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.648][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:47.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.649][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:47.650][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.653][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:47.653][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:47.654][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.655][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:30:47.656][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:47.656][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.658][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:47.658][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:47.658][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:47.658][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:47.658][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:47.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:47.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:47.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.662][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.663][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.664][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:47.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:47.665][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.666][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.666][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:30:47.668][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.668][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 23:30:47.669][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.670][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:47.670][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.671][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.672][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.673][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:47.674][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:47.675][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.675][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:30:47.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:47.677][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.677][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.678][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.679][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:47.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.681][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:47.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.683][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:47.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:47.685][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.686][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.687][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:30:47.688][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.689][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:47.689][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.690][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:47.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.691][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.692][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.693][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:47.694][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:47.695][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.696][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:30:47.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:47.697][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.698][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.698][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.699][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:47.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.701][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:47.702][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.703][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.704][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.704][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:47.705][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:47.705][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.706][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.709][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:47.709][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.710][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[2024-11-19 23:30:47.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.713][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[2024-11-19 23:30:47.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.766][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:30:47.770][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:30:47.771][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:30:47.772][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:30:47.773][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:30:47.774][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:47.775][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:47.776][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:47.777][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:30:47.778][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:47.779][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:47.780][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:30:47.781][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:47.781][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:47.782][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:30:47.783][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:47.784][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:30:47.785][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:30:47.786][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:30:47.787][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:30:47.788][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:30:47.789][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:30:47.790][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:30:47.791][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:30:47.792][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:30:47.793][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:30:47.794][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:30:47.795][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:30:47.796][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:30:47.797][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:30:47.798][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:30:47.799][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:30:47.800][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:30:47.801][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:30:47.802][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:30:47.803][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:30:47.804][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:30:47.805][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:30:47.806][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:30:47.807][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:30:47.808][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:30:47.809][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:30:47.810][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:30:47.811][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:30:47.812][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:30:47.813][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:30:47.814][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:30:47.815][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:30:47.816][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:30:47.817][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:30:47.818][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:30:47.818][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:30:47.819][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:30:47.820][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:30:47.821][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:30:47.822][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:30:47.823][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:30:47.824][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:30:47.825][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:30:47.826][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:30:47.827][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:30:47.828][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:30:47.829][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:30:47.830][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:30:47.831][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:30:47.832][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:30:47.833][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:30:47.834][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:30:47.835][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:30:47.836][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:30:47.837][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:30:47.838][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:30:47.839][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:30:47.840][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:30:47.841][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:30:47.842][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:30:47.843][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:30:47.844][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:30:47.845][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:30:47.846][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:30:47.847][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:30:47.848][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:30:47.849][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:30:47.853][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:30:47.854][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:47.856][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:47.857][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.858][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.859][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[2024-11-19 23:30:47.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.870][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[2024-11-19 23:30:47.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.888][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[2024-11-19 23:30:47.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.931][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[2024-11-19 23:30:47.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:47.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:47.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:47.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:47.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:47.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:47.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:47.940][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:47.948][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:47.950][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.950][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.952][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:47.953][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.953][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-11-19 23:30:47.954][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.955][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.955][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:30:47.956][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:47.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.957][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-11-19 23:30:47.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-11-19 23:30:47.959][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-11-19 23:30:47.960][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:47.960][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:47.960][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-11-19 23:30:47.960][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-11-19 23:30:47.961][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:30:47.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.963][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:47.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:47.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:47.965][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:47.965][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-19 23:30:47.965][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-11-19 23:30:47.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:47.967][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:47.967][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:47.968][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:47.972][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-11-19 23:30:47.973][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:47.975][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:47.976][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:47.977][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:47.994][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:47.995][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-11-19 23:30:47.998][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:48.033][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:48.036][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:48.037][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:48.038][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-11-19 23:30:48.039][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-11-19 23:30:48.039][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-19 23:30:48.039][self$setPropertyValue] Setting property "urls" to "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-11-19 23:30:48.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:48.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:48.041][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-11-19 23:30:48.042][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-11-19 23:30:48.043][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:48.056][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:48.057][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:48.057][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:48.058][private$addConnectorRules] Create new rule for URL "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:48.059][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:48.060][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-11-19 23:30:48.065][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.066][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-11-19 23:30:48.067][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:48.067][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:48.072][loadFileContents] Loaded 1 files from cache: [1]: "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-11-19 23:30:48.073][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:48.076][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:48.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:48.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:48.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:48.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:48.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:48.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:48.088][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.TRACE[2024-11-19 23:30:48.095][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.096][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.097][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.110][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.110][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.112][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.130][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.133][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.134][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.135][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.139][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.140][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.141][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.142][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.154][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.158][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.159][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.160][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.164][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.165][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.166][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.167][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.170][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.171][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.172][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.173][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.176][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.177][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.178][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.182][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.182][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.184][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.185][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.187][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.188][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.189][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.194][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.196][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.201][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.205][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.206][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.207][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.211][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.211][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.213][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.216][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.217][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.218][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.219][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.222][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.223][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.225][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.228][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:48.229][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.230][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.231][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:48.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.269][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.272][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.274][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.277][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.280][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.283][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.302][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.313][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.324][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.327][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.329][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.332][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.338][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.340][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.364][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.366][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.369][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.390][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.393][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.396][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.399][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.402][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.404][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.407][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.412][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:48.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.423][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:48.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.456][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.459][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.465][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:48.484][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-19 23:30:48.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:48.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:48.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:48.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:48.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.513][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.539][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.542][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:48.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.563][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.564][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.565][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.577][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.580][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.583][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.583][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.585][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.585][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.602][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.602][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.604][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.612][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.615][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.617][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.620][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.621][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.622][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.623][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.641][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.654][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.657][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.659][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.662][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.663][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.664][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.665][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.681][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.682][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.683][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.693][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.698][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.701][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.702][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.703][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.704][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.719][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.720][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.722][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.722][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.730][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.733][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.738][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.739][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.740][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.741][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.761][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.764][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.772][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.775][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.780][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.781][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.782][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.796][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.799][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.799][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.801][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.817][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.818][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.819][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.827][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.830][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.833][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.836][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.836][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.838][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.838][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:48.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:48.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.859][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.860][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.861][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.878][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.879][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.880][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.888][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.891][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.894][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.896][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.897][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.898][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.899][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.907][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:48.908][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:48.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.909][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.912][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.913][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:48.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.914][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.917][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.918][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:48.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.919][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.923][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:48.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.924][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.927][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.928][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:48.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.929][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.932][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.933][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:48.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.935][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.938][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.938][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:48.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.940][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.943][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.944][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:48.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.945][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.953][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:48.954][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:48.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.955][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.959][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:48.959][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:48.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.961][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.964][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.966][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.969][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.970][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.972][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.975][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.976][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:48.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.977][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.980][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.981][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.982][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.985][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.986][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.987][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.990][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.991][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:48.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.996][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.997][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:48.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.998][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.001][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:49.002][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:49.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.003][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:49.009][biodb::testThat]
biodb.INFO [2024-11-19 23:30:49.009][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-19 23:30:49.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:49.011][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:49.021][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-19 23:30:49.026][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-19 23:30:49.031][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.032][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-19 23:30:49.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-11-19 23:30:49.034][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:49.038][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-11-19 23:30:49.039][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:49.061][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:49.062][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:49.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:49.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:49.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:49.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:49.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:49.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:49.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:49.073][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.074][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.075][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.079][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.080][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.081][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.082][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.085][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.086][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.087][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.088][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.091][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.092][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.094][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.097][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.099][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.102][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.103][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.105][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.108][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.109][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.110][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.111][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.114][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.115][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.116][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.117][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.120][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.120][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.122][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.123][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.125][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.126][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.127][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.128][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.131][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:49.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:49.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.133][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:49.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:49.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.137][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:49.138][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:49.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.139][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:49.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:49.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.143][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.145][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.150][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.154][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.159][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.161][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.485][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.486][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.488][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.491][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:49.492][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:49.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.493][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:49.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:49.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.498][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:49.498][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.500][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.501][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:49.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.512][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.515][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.518][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:49.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.521][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.523][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:49.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:49.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:49.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.558][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:49.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:49.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.569][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.579][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:49.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:49.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.584][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:49.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:49.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:49.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:49.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:49.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:49.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:49.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:49.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:49.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.606][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.609][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.611][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:49.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:49.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.630][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.633][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.636][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:49.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.638][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.641][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.644][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:49.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.649][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:49.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:49.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:49.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:49.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:49.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.665][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:49.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:49.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:49.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:49.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:49.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.695][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:49.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:49.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:49.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.714][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-19 23:30:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-19 23:30:49.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-19 23:30:49.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-19 23:30:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-19 23:30:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-19 23:30:49.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-19 23:30:49.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:49.728][biodb::testThat]
biodb.INFO [2024-11-19 23:30:49.729][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-19 23:30:49.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:49.730][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:49.732][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.733][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.734][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.735][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-11-19 23:30:49.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.768][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-11-19 23:30:49.769][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-19 23:30:49.770][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-19 23:30:49.770][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-19 23:30:49.771][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.772][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.773][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:49.774][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.775][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:49.776][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:49.777][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:49.778][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:49.778][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:49.779][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:49.780][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-19 23:30:49.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.792][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:49.793][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:49.794][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-11-19 23:30:49.801][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.802][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.803][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.804][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-11-19 23:30:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.815][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.822][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[2024-11-19 23:30:49.864][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-11-19 23:30:49.865][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-11-19 23:30:49.866][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-11-19 23:30:49.876][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.877][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.878][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:49.879][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.879][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:49.890][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:49.891][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:49.892][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:49.892][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:49.893][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:49.894][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-19 23:30:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.898][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:49.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.906][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:49.907][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:49.907][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-11-19 23:30:49.915][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.916][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.917][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.918][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-11-19 23:30:49.926][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.929][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.932][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.936][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-11-19 23:30:49.937][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-11-19 23:30:49.938][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-11-19 23:30:49.938][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-11-19 23:30:49.939][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.940][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.946][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:49.947][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:49.948][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:49.948][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:49.949][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:49.950][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:49.951][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:49.951][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:49.952][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-19 23:30:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.956][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.959][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.962][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:49.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:49.964][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:49.965][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:49.966][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-11-19 23:30:49.975][biodb::testThat]
biodb.INFO [2024-11-19 23:30:49.976][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-11-19 23:30:49.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:49.977][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:49.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:49.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:49.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:50.000][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-19 23:30:50.000][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-19 23:30:50.004][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-19 23:30:50.006][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:50.007][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:50.009][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:50.010][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:50.011][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:50.012][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:50.013][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:50.013][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:50.014][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:50.015][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:50.016][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-19 23:30:50.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:50.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:50.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:50.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:50.041][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:50.042][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-11-19 23:30:50.056][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.057][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-11-19 23:30:50.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:50.059][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:50.087][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.091][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.095][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:50.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.100][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:50.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:50.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:50.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:50.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:50.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:50.167][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.168][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-19 23:30:50.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:50.169][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.176][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.176][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-19 23:30:50.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:50.178][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.184][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.185][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-19 23:30:50.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:50.186][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:50.189][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-11-19 23:30:52.130][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-11-19 23:30:52.190][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.191][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-19 23:30:52.191][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:52.192][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:52.440][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-11-19 23:30:52.511][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:52.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:52.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.514][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:52.514][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:52.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.517][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:52.517][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:52.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.519][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:52.520][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.520][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-11-19 23:30:52.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:52.522][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:52.523][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-19 23:30:52.557][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-11-19 23:30:52.559][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-11-19 23:30:52.559][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-11-19 23:30:52.560][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-11-19 23:30:52.561][private$doDownload] Downloading HMDB metabolite database at "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-11-19 23:30:52.562][cch$addFilesToCache] Moving files to cache [1]: "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-11-19 23:30:52.563][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-19 23:30:52.565][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:52.566][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-19 23:30:52.567][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-11-19 23:30:52.569][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker21789d6861fc98marker".
biodb.TRACE[2024-11-19 23:30:52.569][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-11-19 23:30:52.570][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:52.571][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-11-19 23:30:52.572][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-11-19 23:30:52.573][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-11-19 23:30:52.574][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-19 23:30:52.574][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2024-11-19 23:30:52.594][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-11-19 23:30:52.594][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-11-19 23:30:52.595][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-11-19 23:30:52.596][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2024-11-19 23:30:52.602][self$addFilesToCache] Moving files to cache [2]: "/media/volume/teran2_disk/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /media/volume/teran2_disk/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-11-19 23:30:52.603][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-11-19 23:30:52.604][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:52.604][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-11-19 23:30:52.606][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker21789d4dcdb9bmarker".
biodb.TRACE[2024-11-19 23:30:52.607][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-11-19 23:30:52.607][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-11-19 23:30:52.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-19 23:30:52.620][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:30:52.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:30:52.622][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:52.623][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.624][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:52.625][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:52.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:52.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:52.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:52.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:52.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:52.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.633][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.TRACE[2024-11-19 23:30:52.634][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.637][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:52.656][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-11-19 23:30:52.657][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-19 23:30:52.668][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.696][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-19 23:30:52.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:52.701][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:52.707][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2024-11-19 23:30:52.708][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2024-11-19 23:30:52.709][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-19 23:30:52.710][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.711][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-19 23:30:52.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2024-11-19 23:30:52.713][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:30:52.714][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:30:52.715][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:52.716][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.717][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:52.718][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:52.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:52.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:52.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:52.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:52.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:52.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:52.828][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.831][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:52.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:52.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:52.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:52.851][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-11-19 23:30:52.852][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-19 23:30:52.852][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2024-11-19 23:30:52.861][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.862][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-11-19 23:30:52.863][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:52.863][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.883][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.884][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-11-19 23:30:52.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:52.885][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:52.887][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.888][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.889][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:52.890][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.891][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:52.892][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:52.892][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:52.893][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:52.894][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2024-11-19 23:30:52.899][biodb::testThat]
biodb.INFO [2024-11-19 23:30:52.900][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-11-19 23:30:52.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:52.901][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:52.903][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.904][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.905][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:52.906][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:52.907][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:52.908][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:52.909][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:52.909][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:52.910][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2024-11-19 23:30:52.920][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:52.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:52.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.922][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.923][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:52.926][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:52.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.930][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.936][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:52.938][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:52.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.940][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:52.941][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:30:52.942][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-11-19 23:30:52.950][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-11-19 23:30:52.951][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:30:52.952][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:52.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:52.953][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:52.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:52.954][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.955][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.INFO [2024-11-19 23:30:52.959][biodb::testContext]
biodb.INFO [2024-11-19 23:30:52.959][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:52.960][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2024-11-19 23:30:52.961][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:52.962][biodb::testContext]
biodb.INFO [2024-11-19 23:30:52.965][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:52.966][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:52.969][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:52.970][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:30:52.971][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:30:52.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:52.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:52.974][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:30:52.975][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:30:52.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:52.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:52.977][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:30:52.978][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:30:52.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:52.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:52.981][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:30:52.981][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:30:52.989][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:30:52.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:52.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:52.992][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:30:52.993][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:30:52.994][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:30:52.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:52.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:52.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:52.997][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:30:52.998][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:30:52.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:52.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.000][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:30:53.001][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:30:53.002][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:30:53.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.005][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:30:53.005][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.008][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:30:53.009][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:30:53.010][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.013][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:53.013][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:30:53.014][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:30:53.015][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:30:53.016][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:30:53.016][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:30:53.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.019][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:30:53.020][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:30:53.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.022][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:30:53.023][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:30:53.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.026][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:30:53.027][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:30:53.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.029][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:30:53.030][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:30:53.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.033][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:30:53.033][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:30:53.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.036][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:53.037][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:30:53.040][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:30:53.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.042][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:30:53.043][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:30:53.044][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:30:53.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.047][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:30:53.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.049][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 23:30:53.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.050][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.051][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.052][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.052][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.053][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.054][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:53.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.055][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.056][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:30:53.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.058][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.058][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.059][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:53.059][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:53.059][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:53.059][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:53.059][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:53.060][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:53.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.062][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.064][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.065][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.065][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.073][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.075][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:30:53.076][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.077][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:53.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.079][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.080][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.081][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.082][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.082][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:53.083][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.084][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.084][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:30:53.085][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.086][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.087][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.087][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:53.087][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:53.087][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:53.087][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:53.087][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:53.088][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:53.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.090][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.093][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.095][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.096][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.097][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:30:53.098][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.099][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 23:30:53.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.100][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.101][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.102][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.103][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.103][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.104][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:53.105][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.105][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.106][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:30:53.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.108][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.108][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.109][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.110][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:53.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.112][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.115][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.117][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.117][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.118][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:30:53.119][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.120][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:53.121][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.122][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.122][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.123][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.124][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.124][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.125][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:53.126][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.127][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.127][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:30:53.128][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.129][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.129][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.130][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.131][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:53.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.136][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.138][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.139][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:53.140][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.147][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[2024-11-19 23:30:53.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.160][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[2024-11-19 23:30:53.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.203][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:30:53.204][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:30:53.205][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:30:53.206][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:30:53.207][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:30:53.208][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:53.209][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:53.210][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:53.211][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:30:53.212][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:53.213][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:53.214][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:30:53.215][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:53.216][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:53.217][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:30:53.218][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:53.219][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:30:53.220][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:30:53.221][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:30:53.222][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:30:53.223][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:30:53.224][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:30:53.225][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:30:53.226][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:30:53.227][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:30:53.235][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:30:53.236][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:30:53.237][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:30:53.238][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:30:53.239][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:30:53.240][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:30:53.241][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:30:53.242][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:30:53.243][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:30:53.244][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:30:53.245][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:30:53.246][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:30:53.247][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:30:53.248][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:30:53.249][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:30:53.250][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:30:53.252][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:30:53.253][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:30:53.254][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:30:53.255][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:30:53.256][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:30:53.257][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:30:53.258][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:30:53.259][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:30:53.260][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:30:53.261][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:30:53.262][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:30:53.263][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:30:53.264][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:30:53.265][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:30:53.266][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:30:53.267][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:30:53.268][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:30:53.269][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:30:53.270][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:30:53.271][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:30:53.272][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:30:53.273][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:30:53.274][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:30:53.275][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:30:53.276][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:30:53.277][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:30:53.278][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:30:53.279][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:30:53.280][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:30:53.281][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:30:53.282][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:30:53.283][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:30:53.284][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:30:53.285][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:30:53.286][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:30:53.287][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:30:53.288][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:30:53.289][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:30:53.290][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:30:53.291][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:30:53.292][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:30:53.293][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:30:53.295][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:30:53.296][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:53.297][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:53.297][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.299][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.315][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[2024-11-19 23:30:53.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.382][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[2024-11-19 23:30:53.384][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:53.385][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:53.393][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.394][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.395][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.396][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.397][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-11-19 23:30:53.398][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.398][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.399][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:30:53.400][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.401][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.401][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-11-19 23:30:53.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-11-19 23:30:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-11-19 23:30:53.404][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.406][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:53.406][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-11-19 23:30:53.406][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-11-19 23:30:53.406][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:30:53.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.412][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-19 23:30:53.412][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-11-19 23:30:53.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.413][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.414][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.414][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.415][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-11-19 23:30:53.416][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:53.418][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:53.419][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:53.420][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:53.422][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:53.423][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-11-19 23:30:53.424][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:53.425][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:53.426][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:53.427][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:53.428][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-11-19 23:30:53.428][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-11-19 23:30:53.429][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-19 23:30:53.429][self$setPropertyValue] Setting property "urls" to "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-11-19 23:30:53.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.431][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-11-19 23:30:53.432][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-11-19 23:30:53.433][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:53.434][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:53.435][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:53.435][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:53.436][private$addConnectorRules] Create new rule for URL "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:53.437][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:53.438][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-11-19 23:30:53.439][biodb::testThat]
biodb.INFO [2024-11-19 23:30:53.440][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2024-11-19 23:30:53.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:53.441][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:53.444][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:53.445][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:53.446][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:53.447][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:53.448][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:53.449][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:53.450][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:53.451][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:53.451][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:53.453][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-11-19 23:30:53.458][biodb::testThat]
biodb.INFO [2024-11-19 23:30:53.458][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2024-11-19 23:30:53.459][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:53.460][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:53.461][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-11-19 23:30:53.462][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-19 23:30:53.463][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:53.464][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-19 23:30:53.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-11-19 23:30:53.466][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:53.467][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-11-19 23:30:53.468][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:53.469][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:53.470][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:53.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:53.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.485][FUN] Functions in observer BiodbConfig: [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[2024-11-19 23:30:53.488][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.489][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.490][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.494][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.495][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.497][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.500][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.501][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.502][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.503][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.506][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.507][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.508][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.509][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.514][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.518][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.519][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.524][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.525][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.526][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.527][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.530][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.531][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.532][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.533][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.536][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.537][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.538][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.542][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.543][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.548][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:53.549][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:53.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.550][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:53.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.554][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:53.555][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:53.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.562][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.567][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.567][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.569][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.573][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.575][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.579][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.581][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.585][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:53.586][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:53.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.587][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.588][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:53.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:53.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.591][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:53.592][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:53.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:53.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:53.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.597][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:53.598][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.599][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.600][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:53.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.611][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.617][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:53.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.620][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.623][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.626][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.658][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.661][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:53.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:53.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:53.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:53.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.683][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:53.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:53.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:53.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:53.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.689][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:53.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:53.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.692][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:53.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:53.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:53.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:53.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:53.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.721][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:53.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:53.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.744][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.747][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.752][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.755][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.758][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:53.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.763][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:53.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:53.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.766][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:53.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:53.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.780][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:53.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:53.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:53.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:53.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.807][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:53.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:53.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.810][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:53.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:53.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:53.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:53.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:53.836][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-11-19 23:30:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:53.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:53.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:53.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:53.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:53.850][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:30:53.851][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-11-19 23:30:53.852][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-11-19 23:30:53.853][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:30:53.854][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.855][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.856][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-19 23:30:53.859][biodb::testContext]
biodb.INFO [2024-11-19 23:30:53.860][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:53.861][biodb::testContext] Test context - Test search of entries
biodb.INFO [2024-11-19 23:30:53.862][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:53.862][biodb::testContext]
biodb.INFO [2024-11-19 23:30:53.865][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:53.866][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:53.869][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:53.870][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:30:53.871][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.873][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:30:53.874][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.877][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:30:53.883][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.885][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[2024-11-19 23:30:53.886][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:30:53.887][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:30:53.887][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:30:53.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.890][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:30:53.891][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:30:53.892][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.894][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:30:53.895][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:30:53.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.898][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:30:53.898][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:30:53.899][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:30:53.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.902][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:30:53.902][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.905][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:30:53.906][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:30:53.906][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:30:53.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.909][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:53.910][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:30:53.910][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:30:53.911][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:30:53.912][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:30:53.913][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:30:53.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.915][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:30:53.916][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:30:53.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.918][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:30:53.919][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:30:53.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.921][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:30:53.922][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:30:53.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.924][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[2024-11-19 23:30:53.925][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:30:53.925][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:30:53.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.928][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:30:53.929][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:30:53.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.931][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[2024-11-19 23:30:53.931][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:53.932][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:30:53.935][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:30:53.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.938][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:30:53.938][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:30:53.939][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:30:53.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:53.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.942][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:30:53.943][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.944][self$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[2024-11-19 23:30:53.945][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.947][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.948][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.949][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:53.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.950][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.951][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:30:53.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.952][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.953][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.954][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:53.954][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:53.954][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:53.954][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:53.954][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:53.954][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:53.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.961][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.963][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.964][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.967][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.968][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:30:53.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:53.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.973][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.974][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.975][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:53.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.976][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.977][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:30:53.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.978][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.979][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.980][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:53.980][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:53.980][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:53.980][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:53.980][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:53.980][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:53.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.982][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:53.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:53.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:53.984][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.985][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.986][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:53.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:53.987][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.988][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.989][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:30:53.990][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.990][self$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[2024-11-19 23:30:53.991][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.992][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:53.993][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:53.993][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.994][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:53.995][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:53.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:53.997][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:53.997][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:30:53.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:53.999][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:53.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.000][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:54.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:54.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:54.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:54.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:54.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:54.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.005][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:54.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:54.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.008][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.009][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:30:54.010][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.011][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:54.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:54.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.015][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:54.016][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:54.017][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.017][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:30:54.018][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:54.019][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.019][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.020][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.021][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:54.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:54.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:54.023][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:54.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:54.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:54.025][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.025][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.026][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:54.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:54.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.028][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.033][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:54.033][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.043][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[2024-11-19 23:30:54.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.086][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:30:54.087][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:30:54.088][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:30:54.089][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:30:54.090][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:30:54.091][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:54.092][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:54.093][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:54.094][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:30:54.095][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:54.096][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:54.097][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:30:54.098][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:54.103][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:54.104][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:30:54.105][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:54.106][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:30:54.107][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:30:54.108][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:30:54.109][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:30:54.110][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:30:54.111][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:30:54.112][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:30:54.113][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:30:54.114][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:30:54.115][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:30:54.116][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:30:54.117][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:30:54.118][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:30:54.119][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:30:54.120][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:30:54.121][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:30:54.122][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:30:54.123][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:30:54.124][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:30:54.125][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:30:54.125][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:30:54.126][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:30:54.127][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:30:54.128][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:30:54.129][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:30:54.130][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:30:54.131][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:30:54.132][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:30:54.133][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:30:54.134][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:30:54.135][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:30:54.136][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:30:54.137][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:30:54.138][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:30:54.139][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:30:54.140][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:30:54.141][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:30:54.142][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:30:54.143][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:30:54.144][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:30:54.145][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:30:54.146][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:30:54.147][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:30:54.148][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:30:54.149][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:30:54.150][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:30:54.150][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:30:54.151][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:30:54.152][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:30:54.153][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:30:54.154][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:30:54.155][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:30:54.156][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:30:54.157][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:30:54.158][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:30:54.159][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:30:54.160][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:30:54.161][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:30:54.162][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:30:54.163][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:30:54.164][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:30:54.165][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:30:54.166][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:30:54.167][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:30:54.168][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:30:54.173][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:30:54.174][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:30:54.175][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:30:54.176][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:54.177][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:54.178][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.179][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.209][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.DEBUG[2024-11-19 23:30:54.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:54.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.257][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:54.258][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:54.260][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.260][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:54.262][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.263][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-11-19 23:30:54.264][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.264][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.265][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:30:54.266][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:54.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.267][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-11-19 23:30:54.268][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-11-19 23:30:54.269][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:54.270][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:54.270][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-11-19 23:30:54.270][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-11-19 23:30:54.271][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:30:54.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:54.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:54.273][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:54.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:54.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:54.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:54.275][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-19 23:30:54.275][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-11-19 23:30:54.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:54.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:54.277][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:54.278][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:54.279][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-11-19 23:30:54.280][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:54.281][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:54.282][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:54.283][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:54.285][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:54.286][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-11-19 23:30:54.287][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:54.288][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:54.289][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:54.289][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:54.290][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-11-19 23:30:54.291][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-11-19 23:30:54.292][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-19 23:30:54.292][self$setPropertyValue] Setting property "urls" to "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-11-19 23:30:54.292][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:54.293][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:54.294][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-11-19 23:30:54.294][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-11-19 23:30:54.295][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-19 23:30:54.296][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:54.297][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:54.297][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:54.298][private$addConnectorRules] Create new rule for URL "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-19 23:30:54.299][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:54.300][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-11-19 23:30:54.301][biodb::testThat]
biodb.INFO [2024-11-19 23:30:54.301][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2024-11-19 23:30:54.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:54.303][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:54.304][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-11-19 23:30:54.305][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-11-19 23:30:54.306][private$doSearchForEntries] fields VALUES = and
biodb.INFO [2024-11-19 23:30:54.308][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-11-19 23:30:54.309][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-11-19 23:30:54.310][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-11-19 23:30:54.315][private$doDownload] Downloading HMDB metabolite database at "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-11-19 23:30:54.317][cch$addFilesToCache] Moving files to cache [1]: "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-11-19 23:30:54.318][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-19 23:30:54.319][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:54.320][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-19 23:30:54.320][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-11-19 23:30:54.322][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker21789d12c61a7marker".
biodb.TRACE[2024-11-19 23:30:54.322][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-11-19 23:30:54.323][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:54.324][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-11-19 23:30:54.325][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-11-19 23:30:54.326][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-11-19 23:30:54.327][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-19 23:30:54.328][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2024-11-19 23:30:54.330][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-11-19 23:30:54.330][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-11-19 23:30:54.331][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-11-19 23:30:54.332][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2024-11-19 23:30:54.338][self$addFilesToCache] Moving files to cache [2]: "/media/volume/teran2_disk/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /media/volume/teran2_disk/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-11-19 23:30:54.339][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-11-19 23:30:54.340][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:54.340][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-11-19 23:30:54.342][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker21789d7196d1dbmarker".
biodb.TRACE[2024-11-19 23:30:54.342][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-11-19 23:30:54.343][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-19 23:30:54.344][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:54.345][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:54.346][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:54.346][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:54.347][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:54.348][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:54.349][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:54.349][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:54.350][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2024-11-19 23:30:54.351][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-19 23:30:54.352][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-19 23:30:54.353][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:54.354][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-19 23:30:54.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-11-19 23:30:54.356][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:54.358][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-11-19 23:30:54.358][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:54.359][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:54.360][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:54.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:54.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:54.371][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.372][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.373][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.377][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.378][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.379][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.383][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.383][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.385][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.386][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.388][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.389][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.390][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.391][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.401][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.405][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.406][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.407][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.411][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.412][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.413][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.417][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.418][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.419][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.423][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.424][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.425][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.429][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.429][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.431][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.434][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.436][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.440][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.441][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.442][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.446][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.446][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.448][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.451][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.452][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.453][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.457][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.459][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.463][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.463][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.465][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.465][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.468][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.477][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.479][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.484][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:54.485][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.486][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.487][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:54.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.498][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.504][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.506][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.509][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.512][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.531][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.542][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.561][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.563][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.566][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.594][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.599][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.618][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.627][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.634][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.637][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.639][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.642][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.645][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.648][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:54.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.659][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:54.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.676][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:54.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:54.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:54.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:54.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.684][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:54.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:54.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:54.709][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-19 23:30:54.709][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.712][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.718][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:54.720][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:54.721][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:54.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:54.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:54.730][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-11-19 23:30:54.731][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-19 23:30:54.732][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:54.733][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-19 23:30:54.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-11-19 23:30:54.735][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:54.736][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-11-19 23:30:54.737][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:54.738][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:54.739][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-19 23:30:54.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:54.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:54.749][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.751][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.755][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.756][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.757][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.758][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:54.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.761][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.761][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.763][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.764][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.766][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.767][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.768][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.772][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.773][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.774][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.783][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.784][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.785][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.789][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.790][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.791][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.795][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.796][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.798][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.801][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.802][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.803][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.807][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.808][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.809][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.810][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.813][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.815][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.818][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.819][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.820][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.824][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.825][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.826][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.830][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.832][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.835][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.837][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.841][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.842][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.843][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.844][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.846][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.847][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.848][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.849][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.852][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:54.853][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.859][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.860][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-19 23:30:54.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.872][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.875][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:54.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.880][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.885][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-19 23:30:54.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-19 23:30:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.910][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-19 23:30:54.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.918][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-19 23:30:54.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.923][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-19 23:30:54.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.934][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.937][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:54.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:54.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.945][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.948][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.967][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.970][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.991][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.994][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.997][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-19 23:30:54.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:55.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:55.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.006][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:55.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:55.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:55.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-19 23:30:55.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.013][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:55.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:55.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.015][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:55.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:55.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.018][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:55.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:55.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.021][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:55.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.032][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-19 23:30:55.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:55.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:55.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:55.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:55.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:55.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:55.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:55.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:55.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:55.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.049][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:55.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:55.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.052][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:55.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.057][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:55.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-19 23:30:55.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:55.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:55.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.081][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-11-19 23:30:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.085][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.090][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.093][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:55.093][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:55.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:55.105][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-11-19 23:30:55.106][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-11-19 23:30:55.106][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-11-19 23:30:55.108][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:55.109][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:55.110][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:55.111][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:55.111][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:55.112][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:55.113][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:55.114][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:55.114][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:55.115][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:55.116][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-19 23:30:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.120][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.123][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.128][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.131][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.136][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:55.137][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:55.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.144][FUN] Functions in observer BiodbConfig: [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[2024-11-19 23:30:55.144][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.147][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.169][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-11-19 23:30:55.170][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:55.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:55.180][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-11-19 23:30:55.181][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-11-19 23:30:55.181][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-11-19 23:30:55.183][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:55.184][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:55.185][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-19 23:30:55.186][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-19 23:30:55.186][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-19 23:30:55.187][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-19 23:30:55.188][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-19 23:30:55.189][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-19 23:30:55.189][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-19 23:30:55.190][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-19 23:30:55.191][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-19 23:30:55.192][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.195][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.197][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.200][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.206][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.211][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-11-19 23:30:55.212][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2024-11-19 23:30:55.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.218][FUN] Functions in observer BiodbConfig: [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[2024-11-19 23:30:55.219][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.222][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.232][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.236][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.238][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.241][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-19 23:30:55.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-19 23:30:55.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.244][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-19 23:30:55.244][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-19 23:30:55.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.252][FUN] Functions in observer BiodbConfig: [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 [2024-11-19 23:30:55.256][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:30:55.257][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-11-19 23:30:55.258][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-11-19 23:30:55.259][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:30:55.259][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.261][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.262][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
  6.387   0.624   9.267

CHECK results for biodbHmdb on teran2

Summary

Command output

Installation output

Tests output

Example timings