Pierrick Roger
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: devel |
| git_last_commit: d2b9830 |
| git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbHmdb |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz |
| StartedAt: 2025-01-24 20:24:46 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 20:25:35 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 49.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘biodbHmdb’ ... ** this is package ‘biodbHmdb’ version ‘1.13.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c EntryMaker.cpp -o EntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c FileEntryMaker.cpp -o FileEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c TagDetector.cpp -o TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c XmlSplitter.cpp -o XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-100-TagDetector.cpp -o test-100-TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help No man pages found in package ‘biodbHmdb’ *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-01-24 20:25:18.045][biodb::testContext]
biodb.INFO [2025-01-24 20:25:18.047][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:18.048][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-01-24 20:25:18.049][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:18.050][biodb::testContext]
biodb.INFO [2025-01-24 20:25:18.051][biodb::testThat]
biodb.INFO [2025-01-24 20:25:18.052][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2025-01-24 20:25:18.053][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:18.054][biodb::testThat]
biodb.INFO [2025-01-24 20:25:18.143][biodb::testContext]
biodb.INFO [2025-01-24 20:25:18.144][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:18.145][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-01-24 20:25:18.146][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:18.147][biodb::testContext]
biodb.INFO [2025-01-24 20:25:18.162][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-24 20:25:18.165][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-24 20:25:18.174][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:18.175][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-24 20:25:18.176][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-24 20:25:18.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.181][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-24 20:25:18.220][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-24 20:25:18.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.224][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-24 20:25:18.225][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-24 20:25:18.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.229][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-24 20:25:18.230][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-24 20:25:18.231][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-24 20:25:18.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.234][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[2025-01-24 20:25:18.235][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-24 20:25:18.236][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-24 20:25:18.237][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-24 20:25:18.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.241][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-24 20:25:18.242][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-24 20:25:18.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.246][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-24 20:25:18.247][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-24 20:25:18.248][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-24 20:25:18.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.252][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-24 20:25:18.253][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-24 20:25:18.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.256][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[2025-01-24 20:25:18.257][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-24 20:25:18.258][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-24 20:25:18.259][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-24 20:25:18.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.263][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-24 20:25:18.264][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-24 20:25:18.265][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-24 20:25:18.266][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-24 20:25:18.267][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-24 20:25:18.268][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-24 20:25:18.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.272][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-24 20:25:18.273][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-24 20:25:18.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.277][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-24 20:25:18.278][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-24 20:25:18.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.281][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-24 20:25:18.283][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-24 20:25:18.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.286][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-24 20:25:18.287][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-24 20:25:18.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.291][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-24 20:25:18.292][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-24 20:25:18.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.296][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-24 20:25:18.297][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-24 20:25:18.301][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-24 20:25:18.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.304][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[2025-01-24 20:25:18.305][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-24 20:25:18.306][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-24 20:25:18.307][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-24 20:25:18.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.314][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-24 20:25:18.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.367][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-24 20:25:18.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:18.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.374][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-24 20:25:18.375][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:18.376][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.377][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-24 20:25:18.378][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:18.379][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.380][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.381][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:18.381][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-24 20:25:18.381][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-24 20:25:18.381][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-24 20:25:18.381][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-24 20:25:18.382][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:18.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:18.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.393][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.394][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:18.395][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:18.396][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.397][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.398][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-24 20:25:18.400][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.401][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-24 20:25:18.402][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:18.403][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.404][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.407][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-24 20:25:18.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:18.409][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.410][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-24 20:25:18.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:18.412][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.413][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.414][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:18.414][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-24 20:25:18.414][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-24 20:25:18.414][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-24 20:25:18.414][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-24 20:25:18.415][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:18.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:18.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.421][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:18.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:18.424][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.425][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.426][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-24 20:25:18.427][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.428][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-24 20:25:18.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.430][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:18.431][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.432][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.433][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.435][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-24 20:25:18.436][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:18.437][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.438][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-24 20:25:18.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:18.440][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.441][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.442][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:18.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.445][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:18.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.449][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:18.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:18.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.453][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.454][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-24 20:25:18.456][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.457][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-24 20:25:18.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.458][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:18.459][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.460][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.461][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.462][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.463][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-24 20:25:18.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:18.465][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.466][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-24 20:25:18.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:18.468][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.469][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.470][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:18.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:18.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.478][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.478][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:18.479][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:18.480][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.481][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.485][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:18.486][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.544][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[2025-01-24 20:25:18.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.557][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[2025-01-24 20:25:18.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.563][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-24 20:25:18.572][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-24 20:25:18.574][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-24 20:25:18.575][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-24 20:25:18.577][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-24 20:25:18.578][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-24 20:25:18.579][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-24 20:25:18.581][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-24 20:25:18.582][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-24 20:25:18.583][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-24 20:25:18.585][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-24 20:25:18.586][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-24 20:25:18.587][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-24 20:25:18.589][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-24 20:25:18.590][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-24 20:25:18.591][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-24 20:25:18.592][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-24 20:25:18.594][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-24 20:25:18.595][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-24 20:25:18.596][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-24 20:25:18.598][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-24 20:25:18.599][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-24 20:25:18.600][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-24 20:25:18.602][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-24 20:25:18.603][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-24 20:25:18.604][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-24 20:25:18.606][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-24 20:25:18.607][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-24 20:25:18.608][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-24 20:25:18.610][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-24 20:25:18.611][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-24 20:25:18.612][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-24 20:25:18.614][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-24 20:25:18.615][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-24 20:25:18.616][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-24 20:25:18.618][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-24 20:25:18.619][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-24 20:25:18.620][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-24 20:25:18.622][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-24 20:25:18.623][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-24 20:25:18.624][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-24 20:25:18.626][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-24 20:25:18.627][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-24 20:25:18.629][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-24 20:25:18.630][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-24 20:25:18.631][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-24 20:25:18.633][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-24 20:25:18.634][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-24 20:25:18.636][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-24 20:25:18.637][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-24 20:25:18.638][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-24 20:25:18.640][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-24 20:25:18.641][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-24 20:25:18.642][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-24 20:25:18.644][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-24 20:25:18.645][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-24 20:25:18.646][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-24 20:25:18.648][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-24 20:25:18.649][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-24 20:25:18.650][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-24 20:25:18.652][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-24 20:25:18.653][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-24 20:25:18.654][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-24 20:25:18.656][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-24 20:25:18.657][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-24 20:25:18.658][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-24 20:25:18.660][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-24 20:25:18.661][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-24 20:25:18.662][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-24 20:25:18.664][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-24 20:25:18.665][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-24 20:25:18.666][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-24 20:25:18.668][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-24 20:25:18.669][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-24 20:25:18.671][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-24 20:25:18.672][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-24 20:25:18.673][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-24 20:25:18.675][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-24 20:25:18.676][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-24 20:25:18.677][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-24 20:25:18.679][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-24 20:25:18.680][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-24 20:25:18.681][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-24 20:25:18.687][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-24 20:25:18.689][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-24 20:25:18.692][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:18.693][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.695][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.729][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[2025-01-24 20:25:18.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:18.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:18.834][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-24 20:25:18.844][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:18.845][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.847][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.848][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.848][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:18.849][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.850][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-24 20:25:18.851][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.853][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-24 20:25:18.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:18.855][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.856][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-24 20:25:18.857][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-24 20:25:18.858][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-24 20:25:18.859][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:18.860][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:18.860][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-24 20:25:18.860][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-24 20:25:18.861][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-24 20:25:18.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.864][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:18.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:18.866][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:18.867][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:18.868][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-24 20:25:18.868][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-24 20:25:18.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:18.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:18.871][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:18.872][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:18.878][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-24 20:25:18.879][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-24 20:25:18.881][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-24 20:25:18.882][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-24 20:25:18.884][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-24 20:25:18.905][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:18.906][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-24 20:25:18.910][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:18.914][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:18.918][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:18.919][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:18.920][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-24 20:25:18.921][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-01-24 20:25:18.922][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-24 20:25:18.922][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-01-24 20:25:18.923][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:18.924][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:18.925][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-01-24 20:25:18.926][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-01-24 20:25:18.927][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:18.951][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:18.952][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:18.953][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:18.954][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:18.956][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:18.957][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-01-24 20:25:18.964][biodb::testThat]
biodb.INFO [2025-01-24 20:25:18.965][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-01-24 20:25:18.966][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:18.967][biodb::testThat]
biodb.TRACE[2025-01-24 20:25:18.971][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-01-24 20:25:18.973][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:18.976][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:18.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:18.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:18.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:18.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:18.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:18.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:18.992][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.TRACE[2025-01-24 20:25:19.003][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.004][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.006][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.024][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.025][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.026][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.052][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.057][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.058][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.060][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.062][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.066][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.067][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.069][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.070][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.074][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.075][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.077][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.083][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.084][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.085][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.091][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.094][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.095][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.099][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.108][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.110][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.115][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.116][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.118][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.123][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.124][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.126][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.132][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.133][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.134][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.140][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:19.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:19.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.142][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:19.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.148][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.149][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.151][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.159][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.164][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.167][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.172][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.173][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.175][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:19.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:19.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.183][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.184][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:19.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:19.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.188][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:19.189][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.191][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.193][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:19.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.253][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.257][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.261][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.265][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.269][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.296][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.300][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:19.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.337][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.342][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:19.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:19.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:19.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:19.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:19.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.381][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.385][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.421][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.429][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.433][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.437][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.441][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.445][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:19.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:19.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.449][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:19.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:19.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:19.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:19.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.458][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:19.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.474][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:19.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.516][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.520][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.528][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:19.559][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-24 20:25:19.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-24 20:25:19.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-24 20:25:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-24 20:25:19.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-24 20:25:19.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-24 20:25:19.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-24 20:25:19.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.574][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-24 20:25:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-24 20:25:19.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.634][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.638][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.642][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:19.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.665][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.666][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.667][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:19.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:19.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.680][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.684][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.688][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.698][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.699][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.701][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.726][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.727][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.729][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:19.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.742][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.746][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.750][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.754][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.755][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.757][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.758][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:19.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.783][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.786][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:19.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.799][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.811][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.813][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.815][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:19.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.840][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.843][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:19.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:19.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.861][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.865][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.869][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.873][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.874][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.876][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:19.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:19.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.888][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.896][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.900][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.901][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.903][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:19.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:19.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.916][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.920][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.924][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.928][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.929][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.931][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.932][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.958][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:19.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.970][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.981][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.982][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.984][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:19.985][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:19.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:19.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.001][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.009][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.012][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.013][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.015][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.039][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.040][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.058][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.062][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.066][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.067][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.069][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.070][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.097][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.122][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.123][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.124][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.141][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.145][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.149][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.152][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.153][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.155][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.156][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.167][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.168][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.170][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.174][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.175][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.177][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.181][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.182][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.184][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.188][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.189][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.191][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.196][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.197][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.198][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.203][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.204][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.206][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.210][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.211][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.213][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.217][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.218][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.220][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.224][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.225][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.227][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.232][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:20.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:20.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.234][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.239][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.240][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.242][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.246][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.247][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.249][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.253][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.254][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.256][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.263][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.267][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.270][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.274][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.275][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.282][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.286][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.287][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.289][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.293][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.294][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.296][ef$get] fields variable is a list.
biodb.INFO [2025-01-24 20:25:20.302][biodb::testThat]
biodb.INFO [2025-01-24 20:25:20.303][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-24 20:25:20.304][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:20.305][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:20.319][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-24 20:25:20.326][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-24 20:25:20.331][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:20.332][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-24 20:25:20.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-24 20:25:20.336][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-24 20:25:20.338][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-24 20:25:20.339][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-24 20:25:20.363][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:20.364][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:20.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:20.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:20.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:20.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:20.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:20.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:20.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:20.378][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.379][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.381][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.387][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.388][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.389][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.391][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.395][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.396][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.398][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.399][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.403][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.404][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.406][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.407][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.411][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.412][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.414][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.424][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.425][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.427][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.432][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.433][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.435][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.436][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.440][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.441][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.443][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.444][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.448][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.449][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.451][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.456][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.457][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.459][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.461][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.465][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:20.466][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:20.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.467][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:20.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.476][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.481][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.482][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.484][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.490][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.492][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.497][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.500][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.505][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.506][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.508][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.509][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.513][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.516][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.521][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:20.522][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.524][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:20.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.545][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:20.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.553][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.557][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.566][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:20.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:20.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:20.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.597][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:20.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:20.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.624][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.628][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.631][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.635][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:20.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:20.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:20.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.647][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:20.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:20.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:20.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:20.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.673][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.677][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:20.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:20.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.719][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.727][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.731][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:20.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.735][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.742][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:20.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.746][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:20.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.786][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:20.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.790][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:20.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:20.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.797][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:20.824][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-24 20:25:20.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-24 20:25:20.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-24 20:25:20.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-24 20:25:20.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-24 20:25:20.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-24 20:25:20.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-24 20:25:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-24 20:25:20.847][biodb::testThat]
biodb.INFO [2025-01-24 20:25:20.848][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-24 20:25:20.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:20.850][biodb::testThat]
biodb.TRACE[2025-01-24 20:25:20.853][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.856][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:20.857][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-01-24 20:25:20.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:20.896][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-01-24 20:25:20.897][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-24 20:25:20.898][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-24 20:25:20.899][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-24 20:25:20.901][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:20.902][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:20.904][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:20.905][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:20.906][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:20.907][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:20.908][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:20.909][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:20.910][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:20.911][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:20.912][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-24 20:25:20.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:20.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:20.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:20.930][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:20.930][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:20.931][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-24 20:25:20.942][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.943][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.945][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:20.946][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-01-24 20:25:20.957][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.961][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:20.969][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:20.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:20.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:20.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:20.975][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-01-24 20:25:21.027][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-24 20:25:21.028][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-24 20:25:21.029][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-24 20:25:21.043][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.044][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.046][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:21.047][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.048][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:21.063][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:21.064][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:21.065][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:21.066][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:21.067][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:21.068][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-24 20:25:21.070][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:21.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:21.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.074][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:21.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:21.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.082][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:21.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:21.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.086][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:21.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:21.089][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:21.090][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:21.091][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-24 20:25:21.102][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.103][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.105][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:21.106][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-01-24 20:25:21.116][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.120][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.124][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:21.130][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-01-24 20:25:21.132][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-01-24 20:25:21.133][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-24 20:25:21.134][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-24 20:25:21.135][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.137][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.138][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:21.139][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.140][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:21.142][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:21.143][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:21.144][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:21.144][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:21.145][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:21.146][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-24 20:25:21.148][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.152][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.156][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.160][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:21.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:21.164][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:21.165][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:21.165][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-01-24 20:25:21.180][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.181][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-01-24 20:25:21.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:21.183][biodb::testThat]
biodb.TRACE[2025-01-24 20:25:21.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:21.215][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-24 20:25:21.216][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-24 20:25:21.222][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-24 20:25:21.224][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.225][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.227][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:21.228][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:21.229][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:21.230][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:21.231][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:21.232][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:21.233][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:21.234][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:21.235][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-24 20:25:21.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:21.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:21.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:21.252][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:21.253][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-01-24 20:25:21.267][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.268][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-01-24 20:25:21.269][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:21.270][biodb::testThat]
biodb.TRACE[2025-01-24 20:25:21.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.295][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.299][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-24 20:25:21.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-24 20:25:21.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-24 20:25:21.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-24 20:25:21.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.356][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-24 20:25:21.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-24 20:25:21.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-24 20:25:21.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:21.364][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-24 20:25:21.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-24 20:25:21.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:21.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-24 20:25:21.373][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.374][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-24 20:25:21.374][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:21.375][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.383][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.384][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-24 20:25:21.385][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:21.386][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.393][biodb::testThat]
biodb.INFO [2025-01-24 20:25:21.394][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-24 20:25:21.395][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:21.396][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:21.399][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-01-24 20:25:23.317][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-01-24 20:25:23.365][biodb::testThat]
biodb.INFO [2025-01-24 20:25:23.367][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-24 20:25:23.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:23.371][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:23.811][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-01-24 20:25:23.841][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:23.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:23.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.845][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.846][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:23.848][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:23.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.850][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.851][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:23.852][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:23.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.854][ef$get] fields variable is a list.
biodb.INFO [2025-01-24 20:25:23.856][biodb::testThat]
biodb.INFO [2025-01-24 20:25:23.857][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-01-24 20:25:23.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:23.860][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:23.862][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-01-24 20:25:23.932][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-24 20:25:23.934][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:23.936][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-24 20:25:23.953][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-01-24 20:25:23.954][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-24 20:25:23.955][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-24 20:25:23.956][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-24 20:25:23.958][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:23.959][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:23.960][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:23.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:23.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:23.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:23.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:23.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:23.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:23.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:23.972][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:23.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:23.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.976][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:23.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:23.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:23.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:23.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:23.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:23.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:23.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:23.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:24.014][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-01-24 20:25:24.015][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-01-24 20:25:24.071][biodb::testThat]
biodb.INFO [2025-01-24 20:25:24.072][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-01-24 20:25:24.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:24.074][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:24.081][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-01-24 20:25:24.083][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-01-24 20:25:24.084][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-24 20:25:24.085][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.087][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-24 20:25:24.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-01-24 20:25:24.090][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-24 20:25:24.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-24 20:25:24.092][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-24 20:25:24.093][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.094][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:24.095][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:24.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:24.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:24.108][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:24.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:24.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:24.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:24.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:24.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:24.139][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-01-24 20:25:24.140][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-01-24 20:25:24.141][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-01-24 20:25:24.153][biodb::testThat]
biodb.INFO [2025-01-24 20:25:24.154][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-01-24 20:25:24.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:24.156][biodb::testThat]
biodb.INFO [2025-01-24 20:25:24.182][biodb::testThat]
biodb.INFO [2025-01-24 20:25:24.183][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-01-24 20:25:24.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:24.185][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:24.188][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.189][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.190][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:24.192][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.193][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:24.194][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:24.195][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:24.196][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:24.197][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-01-24 20:25:24.204][biodb::testThat]
biodb.INFO [2025-01-24 20:25:24.205][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-01-24 20:25:24.206][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:24.207][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:24.210][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.211][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.212][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:24.214][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:24.215][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:24.216][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:24.217][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:24.218][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:24.219][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-01-24 20:25:24.227][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:24.228][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:24.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.230][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.231][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:24.232][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:24.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.234][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:24.236][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:24.237][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:24.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:24.239][ef$get] fields variable is a list.
biodb.INFO [2025-01-24 20:25:24.240][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-24 20:25:24.241][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-24 20:25:24.249][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-24 20:25:24.250][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-24 20:25:24.251][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.253][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.255][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.256][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.INFO [2025-01-24 20:25:24.259][biodb::testContext]
biodb.INFO [2025-01-24 20:25:24.260][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:24.261][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-01-24 20:25:24.262][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:24.263][biodb::testContext]
biodb.INFO [2025-01-24 20:25:24.267][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-24 20:25:24.269][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-24 20:25:24.273][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:24.274][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-24 20:25:24.275][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-24 20:25:24.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.279][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-24 20:25:24.280][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-24 20:25:24.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.283][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-24 20:25:24.284][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-24 20:25:24.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.294][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-24 20:25:24.295][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-24 20:25:24.296][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-24 20:25:24.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.299][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[2025-01-24 20:25:24.300][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-24 20:25:24.301][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-24 20:25:24.302][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-24 20:25:24.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.306][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-24 20:25:24.307][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-24 20:25:24.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.310][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-24 20:25:24.311][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-24 20:25:24.312][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-24 20:25:24.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.316][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-24 20:25:24.317][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-24 20:25:24.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.320][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[2025-01-24 20:25:24.321][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-24 20:25:24.322][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-24 20:25:24.323][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-24 20:25:24.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.326][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-24 20:25:24.327][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-24 20:25:24.328][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-24 20:25:24.329][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-24 20:25:24.330][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-24 20:25:24.332][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-24 20:25:24.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.336][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-24 20:25:24.337][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-24 20:25:24.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.341][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-24 20:25:24.342][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-24 20:25:24.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.346][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-24 20:25:24.347][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-24 20:25:24.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.351][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-24 20:25:24.353][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-24 20:25:24.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.359][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-24 20:25:24.360][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-24 20:25:24.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.366][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-24 20:25:24.368][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-24 20:25:24.372][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-24 20:25:24.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.378][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-24 20:25:24.380][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-24 20:25:24.382][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-24 20:25:24.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.388][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-24 20:25:24.391][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.392][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-24 20:25:24.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.395][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:24.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.400][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.403][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-24 20:25:24.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:24.407][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.408][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-24 20:25:24.410][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:24.411][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.413][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.414][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:24.414][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-24 20:25:24.414][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-24 20:25:24.414][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-24 20:25:24.414][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-24 20:25:24.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:24.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.420][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:24.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.425][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.427][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.428][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:24.430][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:24.431][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.440][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.443][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-24 20:25:24.446][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.447][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-24 20:25:24.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:24.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.453][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.453][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.455][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-24 20:25:24.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:24.457][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.458][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-24 20:25:24.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:24.460][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.462][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:24.462][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-24 20:25:24.462][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-24 20:25:24.462][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-24 20:25:24.462][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-24 20:25:24.463][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:24.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:24.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.476][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:24.479][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:24.480][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.481][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.483][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-24 20:25:24.485][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.487][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-24 20:25:24.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:24.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.492][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.494][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.495][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-24 20:25:24.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:24.497][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.498][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-24 20:25:24.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:24.501][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.503][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:24.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:24.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.512][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:24.515][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:24.516][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.517][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.518][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-24 20:25:24.521][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.522][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-24 20:25:24.523][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.525][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:24.526][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.527][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.528][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.531][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-24 20:25:24.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:24.533][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.534][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-24 20:25:24.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:24.537][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.539][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:24.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:24.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.549][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:24.551][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:24.552][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.553][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.555][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:24.556][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.563][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[2025-01-24 20:25:24.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.664][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-24 20:25:24.666][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-24 20:25:24.668][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-24 20:25:24.670][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-24 20:25:24.671][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-24 20:25:24.673][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-24 20:25:24.675][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-24 20:25:24.677][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-24 20:25:24.678][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-24 20:25:24.680][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-24 20:25:24.682][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-24 20:25:24.683][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-24 20:25:24.685][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-24 20:25:24.686][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-24 20:25:24.688][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-24 20:25:24.690][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-24 20:25:24.691][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-24 20:25:24.693][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-24 20:25:24.694][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-24 20:25:24.696][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-24 20:25:24.697][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-24 20:25:24.699][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-24 20:25:24.700][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-24 20:25:24.702][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-24 20:25:24.703][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-24 20:25:24.705][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-24 20:25:24.707][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-24 20:25:24.709][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-24 20:25:24.710][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-24 20:25:24.721][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-24 20:25:24.723][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-24 20:25:24.725][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-24 20:25:24.727][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-24 20:25:24.728][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-24 20:25:24.730][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-24 20:25:24.731][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-24 20:25:24.733][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-24 20:25:24.734][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-24 20:25:24.736][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-24 20:25:24.737][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-24 20:25:24.738][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-24 20:25:24.740][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-24 20:25:24.741][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-24 20:25:24.743][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-24 20:25:24.744][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-24 20:25:24.746][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-24 20:25:24.747][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-24 20:25:24.749][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-24 20:25:24.751][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-24 20:25:24.752][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-24 20:25:24.754][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-24 20:25:24.755][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-24 20:25:24.756][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-24 20:25:24.758][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-24 20:25:24.759][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-24 20:25:24.761][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-24 20:25:24.762][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-24 20:25:24.764][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-24 20:25:24.765][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-24 20:25:24.767][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-24 20:25:24.768][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-24 20:25:24.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-24 20:25:24.771][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-24 20:25:24.772][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-24 20:25:24.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-24 20:25:24.775][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-24 20:25:24.777][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-24 20:25:24.778][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-24 20:25:24.780][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-24 20:25:24.781][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-24 20:25:24.783][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-24 20:25:24.784][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-24 20:25:24.786][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-24 20:25:24.787][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-24 20:25:24.789][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-24 20:25:24.790][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-24 20:25:24.792][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-24 20:25:24.793][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-24 20:25:24.795][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-24 20:25:24.797][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-24 20:25:24.798][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-24 20:25:24.800][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-24 20:25:24.801][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-24 20:25:24.803][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-24 20:25:24.805][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-24 20:25:24.806][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:24.807][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.809][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.922][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[2025-01-24 20:25:24.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:24.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:24.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:24.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:24.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:24.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:24.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:24.930][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-24 20:25:24.931][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:24.934][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.935][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.936][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.937][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:24.938][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.939][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-24 20:25:24.940][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.941][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.942][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-24 20:25:24.943][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:24.944][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.945][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-24 20:25:24.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-24 20:25:24.953][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-24 20:25:24.955][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:24.956][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:24.956][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-24 20:25:24.956][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-24 20:25:24.957][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-24 20:25:24.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:24.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:24.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:24.963][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:24.964][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-24 20:25:24.964][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-24 20:25:24.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:24.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:24.966][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:24.967][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:24.969][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-24 20:25:24.970][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-24 20:25:24.972][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-24 20:25:24.973][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-24 20:25:24.975][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-24 20:25:24.978][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:24.979][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-24 20:25:24.980][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:24.982][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:24.983][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:24.984][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:24.985][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-24 20:25:24.986][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-01-24 20:25:24.987][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-24 20:25:24.987][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-01-24 20:25:24.988][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:24.989][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:24.990][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-01-24 20:25:24.991][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-01-24 20:25:24.992][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:24.993][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:24.994][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:24.995][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:24.997][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:24.998][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:24.999][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-01-24 20:25:25.000][biodb::testThat]
biodb.INFO [2025-01-24 20:25:25.001][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-01-24 20:25:25.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:25.003][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:25.007][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:25.009][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:25.010][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:25.012][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:25.012][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:25.014][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:25.015][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:25.016][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:25.017][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:25.020][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-01-24 20:25:25.025][biodb::testThat]
biodb.INFO [2025-01-24 20:25:25.026][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-01-24 20:25:25.027][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:25.028][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:25.030][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-01-24 20:25:25.031][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-24 20:25:25.033][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:25.035][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-24 20:25:25.037][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-01-24 20:25:25.038][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-24 20:25:25.041][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-01-24 20:25:25.042][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-24 20:25:25.043][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:25.045][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:25.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:25.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:25.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:25.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.056][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.TRACE[2025-01-24 20:25:25.060][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.061][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.063][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.074][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.075][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.077][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.078][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.082][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.083][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.085][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.087][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.091][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.092][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.094][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.095][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.102][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.107][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.108][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.110][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.117][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.119][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.120][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.124][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.125][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.133][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.134][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.136][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.137][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.141][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.142][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.144][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.146][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.150][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:25.151][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:25.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.153][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.154][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:25.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:25.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.158][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:25.159][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:25.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.161][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:25.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:25.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.168][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.170][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.175][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.176][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.178][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.188][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.189][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.191][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.196][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:25.197][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:25.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.199][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.201][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:25.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.205][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:25.206][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:25.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.208][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.214][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:25.215][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.217][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.271][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.280][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:25.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.284][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.294][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.298][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:25.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:25.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.349][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:25.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.353][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.357][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.365][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:25.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:25.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:25.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.373][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:25.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.378][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:25.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:25.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:25.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:25.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.386][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:25.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:25.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:25.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:25.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:25.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:25.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:25.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.424][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.432][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:25.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.461][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.470][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:25.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.474][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.478][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.483][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:25.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:25.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:25.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:25.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:25.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.499][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:25.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.515][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:25.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:25.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:25.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.545][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:25.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:25.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.549][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:25.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:25.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.557][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:25.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:25.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:25.584][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-01-24 20:25:25.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:25.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:25.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:25.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:25.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-24 20:25:25.603][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-24 20:25:25.604][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-24 20:25:25.605][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-24 20:25:25.606][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-24 20:25:25.607][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:25.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:25.609][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.611][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-24 20:25:25.615][biodb::testContext]
biodb.INFO [2025-01-24 20:25:25.616][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:25.617][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-01-24 20:25:25.618][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-24 20:25:25.619][biodb::testContext]
biodb.INFO [2025-01-24 20:25:25.623][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-24 20:25:25.624][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-24 20:25:25.628][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:25.629][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-24 20:25:25.635][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-24 20:25:25.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.639][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-24 20:25:25.640][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-24 20:25:25.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.644][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-24 20:25:25.645][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-24 20:25:25.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.649][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-24 20:25:25.649][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-24 20:25:25.651][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-24 20:25:25.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.654][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-24 20:25:25.655][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-24 20:25:25.656][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-24 20:25:25.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.660][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-24 20:25:25.661][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-24 20:25:25.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.664][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-24 20:25:25.665][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-24 20:25:25.666][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-24 20:25:25.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.670][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-24 20:25:25.671][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-24 20:25:25.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.674][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-24 20:25:25.675][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-24 20:25:25.676][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-24 20:25:25.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.680][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-24 20:25:25.681][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-24 20:25:25.682][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-24 20:25:25.683][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-24 20:25:25.684][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-24 20:25:25.685][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-24 20:25:25.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.688][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-24 20:25:25.689][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-24 20:25:25.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.693][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-24 20:25:25.694][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-24 20:25:25.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.697][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-24 20:25:25.698][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-24 20:25:25.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.702][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-24 20:25:25.703][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-24 20:25:25.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.707][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-24 20:25:25.708][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-24 20:25:25.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.711][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-24 20:25:25.712][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-24 20:25:25.716][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-24 20:25:25.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.719][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-24 20:25:25.721][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-24 20:25:25.722][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-24 20:25:25.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.725][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-24 20:25:25.727][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.728][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-24 20:25:25.729][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:25.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.733][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.734][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.735][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-24 20:25:25.736][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:25.741][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.742][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-24 20:25:25.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:25.745][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.746][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.747][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:25.747][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-24 20:25:25.747][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-24 20:25:25.747][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-24 20:25:25.747][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-24 20:25:25.748][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:25.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.750][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:25.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.754][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.755][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:25.756][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:25.757][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.758][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.759][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-24 20:25:25.761][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.762][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-24 20:25:25.763][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.764][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:25.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.767][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.768][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-24 20:25:25.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:25.771][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.772][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-24 20:25:25.773][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:25.773][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.774][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.775][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:25.775][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-24 20:25:25.775][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-24 20:25:25.775][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-24 20:25:25.775][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-24 20:25:25.777][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:25.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:25.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.783][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.784][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:25.785][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:25.786][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.787][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.788][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-24 20:25:25.790][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.791][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-24 20:25:25.792][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:25.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.796][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.798][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-24 20:25:25.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:25.800][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.801][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-24 20:25:25.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:25.803][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.804][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.804][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.805][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:25.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:25.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.811][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.812][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.813][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:25.814][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:25.815][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.816][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.817][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-24 20:25:25.819][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.820][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-24 20:25:25.821][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.822][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:25.823][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.824][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.825][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.826][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.827][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-24 20:25:25.828][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:25.829][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.830][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-24 20:25:25.831][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:25.832][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.833][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:25.834][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.835][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-24 20:25:25.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:25.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:25.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:25.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:25.842][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.847][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:25.848][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:25.849][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:25.850][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:25.851][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:25.852][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.918][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[2025-01-24 20:25:25.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.922][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[2025-01-24 20:25:25.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:25.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:25.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:25.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:25.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:25.927][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-24 20:25:25.929][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-24 20:25:25.930][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-24 20:25:25.932][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-24 20:25:25.933][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-24 20:25:25.934][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-24 20:25:25.936][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-24 20:25:25.937][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-24 20:25:25.938][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-24 20:25:25.940][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-24 20:25:25.941][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-24 20:25:25.942][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-24 20:25:25.944][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-24 20:25:25.950][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-24 20:25:25.952][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-24 20:25:25.953][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-24 20:25:25.954][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-24 20:25:25.956][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-24 20:25:25.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-24 20:25:25.958][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-24 20:25:25.960][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-24 20:25:25.961][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-24 20:25:25.962][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-24 20:25:25.964][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-24 20:25:25.965][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-24 20:25:25.966][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-24 20:25:25.967][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-24 20:25:25.969][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-24 20:25:25.970][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-24 20:25:25.971][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-24 20:25:25.973][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-24 20:25:25.974][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-24 20:25:25.975][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-24 20:25:25.977][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-24 20:25:25.978][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-24 20:25:25.979][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-24 20:25:25.981][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-24 20:25:25.982][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-24 20:25:25.984][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-24 20:25:25.985][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-24 20:25:25.986][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-24 20:25:25.988][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-24 20:25:25.989][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-24 20:25:25.990][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-24 20:25:25.992][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-24 20:25:25.993][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-24 20:25:25.994][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-24 20:25:25.996][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-24 20:25:25.997][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-24 20:25:25.998][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-24 20:25:26.000][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-24 20:25:26.001][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-24 20:25:26.002][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-24 20:25:26.004][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-24 20:25:26.005][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-24 20:25:26.006][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-24 20:25:26.008][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-24 20:25:26.009][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-24 20:25:26.011][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-24 20:25:26.012][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-24 20:25:26.013][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-24 20:25:26.015][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-24 20:25:26.016][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-24 20:25:26.017][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-24 20:25:26.019][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-24 20:25:26.020][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-24 20:25:26.021][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-24 20:25:26.023][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-24 20:25:26.024][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-24 20:25:26.025][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-24 20:25:26.027][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-24 20:25:26.028][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-24 20:25:26.029][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-24 20:25:26.031][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-24 20:25:26.032][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-24 20:25:26.033][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-24 20:25:26.035][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-24 20:25:26.036][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-24 20:25:26.037][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-24 20:25:26.039][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-24 20:25:26.040][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-24 20:25:26.042][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-24 20:25:26.043][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-24 20:25:26.050][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-24 20:25:26.051][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-24 20:25:26.053][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-24 20:25:26.053][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.055][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-24 20:25:26.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.165][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-24 20:25:26.167][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:26.169][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:26.170][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-24 20:25:26.170][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:26.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-24 20:25:26.172][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:26.173][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-24 20:25:26.174][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:26.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-24 20:25:26.176][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-24 20:25:26.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-24 20:25:26.178][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:26.179][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-24 20:25:26.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-24 20:25:26.181][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-24 20:25:26.182][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-24 20:25:26.183][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-24 20:25:26.183][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-24 20:25:26.183][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-24 20:25:26.184][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-24 20:25:26.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:26.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:26.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-24 20:25:26.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-24 20:25:26.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-24 20:25:26.190][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-24 20:25:26.191][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-24 20:25:26.191][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-24 20:25:26.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:26.192][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:26.193][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-24 20:25:26.194][self$setPropertyValue]
biodb.DEBUG[2025-01-24 20:25:26.196][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-24 20:25:26.197][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-24 20:25:26.198][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-24 20:25:26.200][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-24 20:25:26.201][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-24 20:25:26.205][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:26.205][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-24 20:25:26.207][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:26.208][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:26.209][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:26.210][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:26.211][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-24 20:25:26.212][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-01-24 20:25:26.213][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-24 20:25:26.213][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-01-24 20:25:26.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-24 20:25:26.215][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-24 20:25:26.216][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-01-24 20:25:26.217][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-01-24 20:25:26.218][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-24 20:25:26.219][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:26.221][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:26.221][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:26.223][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-24 20:25:26.224][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-24 20:25:26.225][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-01-24 20:25:26.226][biodb::testThat]
biodb.INFO [2025-01-24 20:25:26.227][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2025-01-24 20:25:26.228][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-24 20:25:26.229][biodb::testThat]
biodb.DEBUG[2025-01-24 20:25:26.231][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-24 20:25:26.232][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-01-24 20:25:26.233][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-01-24 20:25:26.236][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:26.237][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:26.239][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:26.240][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:26.241][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:26.242][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:26.243][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:26.244][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:26.245][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:26.246][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:26.247][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-01-24 20:25:26.249][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-24 20:25:26.254][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-24 20:25:26.256][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:26.258][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-24 20:25:26.259][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-24 20:25:26.261][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-24 20:25:26.262][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-24 20:25:26.263][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-24 20:25:26.265][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:26.266][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:26.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:26.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:26.280][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.281][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.282][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.288][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.289][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.290][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.292][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.296][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.297][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.299][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.300][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.304][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.305][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.307][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.308][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.312][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.313][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.315][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.320][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.321][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.323][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.328][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.329][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.331][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.336][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.337][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.339][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.341][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.345][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.346][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.347][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.349][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.353][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.354][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.356][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.366][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.367][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.369][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.374][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.375][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.376][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.382][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.383][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.384][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.390][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.391][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.393][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.398][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.399][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.401][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.406][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.407][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.409][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.410][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.414][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.415][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.417][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.422][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:26.423][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.425][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.426][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:26.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.442][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.446][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.450][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.454][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.458][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.471][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.533][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.537][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.541][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.555][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.610][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.615][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.619][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.654][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.659][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.667][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.671][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.676][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.680][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.684][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.688][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.692][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:26.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.709][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:26.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.739][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:26.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:26.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.743][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:26.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:26.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:26.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:26.779][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-24 20:25:26.780][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.784][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.788][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:26.797][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:26.798][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:26.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:26.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:26.810][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-01-24 20:25:26.811][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-24 20:25:26.813][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:26.815][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-24 20:25:26.817][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-01-24 20:25:26.818][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-24 20:25:26.819][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-01-24 20:25:26.820][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-24 20:25:26.822][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-24 20:25:26.823][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-24 20:25:26.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:26.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:26.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:26.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:26.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:26.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:26.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:26.843][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.846][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.851][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.852][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.854][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.855][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:26.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.859][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.860][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.862][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.863][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:26.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.867][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.868][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.870][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.872][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:26.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.878][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.884][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.885][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.887][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.892][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.893][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.895][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.896][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:26.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.900][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.901][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.903][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.904][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:26.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.908][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.909][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.911][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:26.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.916][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.917][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.919][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:26.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.925][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.926][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.928][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:26.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:26.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.933][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.936][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.941][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.949][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:26.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.958][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:26.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.964][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.965][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.966][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:26.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:26.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.972][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.973][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.975][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:26.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.980][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.981][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.983][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.985][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:26.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:26.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.989][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:26.990][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.992][ef$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.993][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-24 20:25:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:26.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:26.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:26.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:26.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.009][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:27.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:27.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.013][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:27.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:27.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-24 20:25:27.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-24 20:25:27.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.021][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:27.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:27.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.025][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:27.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.029][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-24 20:25:27.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-24 20:25:27.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:27.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:27.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:27.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:27.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-24 20:25:27.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-24 20:25:27.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:27.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:27.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:27.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:27.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-24 20:25:27.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:27.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:27.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:27.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:27.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:27.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-24 20:25:27.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:27.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:27.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:27.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:27.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:27.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-24 20:25:27.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.088][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:27.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:27.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:27.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:27.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.096][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:27.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-24 20:25:27.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.100][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.104][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.108][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:27.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:27.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:27.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:27.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.120][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-24 20:25:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-24 20:25:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:27.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-24 20:25:27.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-24 20:25:27.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.148][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:27.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.152][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:27.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:27.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.156][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:27.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-24 20:25:27.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:27.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:27.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:27.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:27.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:27.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-24 20:25:27.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.191][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:27.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:27.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.199][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:27.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-24 20:25:27.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.203][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:27.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:27.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:27.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.211][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:27.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-24 20:25:27.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.215][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:27.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:27.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.219][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:27.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:27.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-24 20:25:27.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-24 20:25:27.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.227][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:27.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.243][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-24 20:25:27.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-24 20:25:27.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-24 20:25:27.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-24 20:25:27.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.268][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.272][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:27.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:27.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.285][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:27.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-24 20:25:27.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-24 20:25:27.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-24 20:25:27.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:27.312][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-01-24 20:25:27.314][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.317][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.321][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:27.329][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:27.330][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:27.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:27.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:27.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:27.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:27.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:27.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:27.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:27.370][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-24 20:25:27.372][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-01-24 20:25:27.373][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-01-24 20:25:27.374][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:27.376][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:27.377][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:27.379][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:27.380][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:27.386][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:27.387][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:27.388][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:27.390][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:27.391][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:27.392][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-24 20:25:27.394][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.398][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.402][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.405][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.409][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.413][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:27.422][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:27.423][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:27.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:27.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:27.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:27.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:27.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:27.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:27.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:27.435][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.439][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.443][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.447][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.451][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.455][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.459][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:27.464][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-01-24 20:25:27.465][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:27.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:27.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:27.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:27.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:27.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:27.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:27.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-24 20:25:27.481][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-24 20:25:27.482][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-01-24 20:25:27.483][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-01-24 20:25:27.485][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:27.487][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:27.489][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-24 20:25:27.490][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-24 20:25:27.491][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-24 20:25:27.492][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-24 20:25:27.494][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-24 20:25:27.495][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-24 20:25:27.495][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-24 20:25:27.501][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-24 20:25:27.502][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-24 20:25:27.504][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.509][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.512][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.516][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.520][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.524][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.528][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:27.531][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-01-24 20:25:27.532][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-01-24 20:25:27.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:27.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:27.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:27.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:27.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:27.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:27.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-24 20:25:27.544][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.548][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.551][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.555][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.559][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.563][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-24 20:25:27.567][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-24 20:25:27.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-24 20:25:27.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-24 20:25:27.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-24 20:25:27.571][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-24 20:25:27.572][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-24 20:25:27.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-24 20:25:27.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:27.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:27.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:27.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:27.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:27.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-24 20:25:27.588][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-24 20:25:27.589][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-24 20:25:27.590][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-24 20:25:27.591][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-24 20:25:27.592][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-24 20:25:27.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-24 20:25:27.593][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-24 20:25:27.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-24 20:25:27.595][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-24 20:25:27.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
>
> proc.time()
user system elapsed
8.892 0.470 11.507