Pierrick Roger
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 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 2025-02-04 11:39 -0500 (Tue, 04 Feb 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" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 203/2295 | 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 | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbHmdb |
| Version: 1.13.0 |
| 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: 2025-02-03 20:34:19 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 20:35:08 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 48.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
3. └─testthat::expect_true(!is.na(content))
── Failure ('test_100_generic.R:19:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE
`actual`:
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─testthat::expect_true(nchar(content) > 0)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 241 ]
Error: Test failures
Execution halted
* 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 ERROR, 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.fail
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-02-03 20:34:51.905][biodb::testContext]
biodb.INFO [2025-02-03 20:34:51.907][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:51.908][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-02-03 20:34:51.909][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:51.910][biodb::testContext]
biodb.INFO [2025-02-03 20:34:51.912][biodb::testThat]
biodb.INFO [2025-02-03 20:34:51.913][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2025-02-03 20:34:51.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:51.915][biodb::testThat]
biodb.INFO [2025-02-03 20:34:52.037][biodb::testContext]
biodb.INFO [2025-02-03 20:34:52.039][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:52.040][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-02-03 20:34:52.041][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:52.042][biodb::testContext]
biodb.INFO [2025-02-03 20:34:52.054][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-03 20:34:52.057][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-03 20:34:52.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:52.068][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-03 20:34:52.070][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-03 20:34:52.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.075][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-03 20:34:52.130][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-03 20:34:52.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.136][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-03 20:34:52.137][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-03 20:34:52.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.141][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-03 20:34:52.143][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-03 20:34:52.144][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-03 20:34:52.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.148][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-03 20:34:52.150][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-03 20:34:52.151][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-03 20:34:52.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.156][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-03 20:34:52.157][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-03 20:34:52.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.161][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-03 20:34:52.162][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-03 20:34:52.163][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-03 20:34:52.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.168][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-03 20:34:52.169][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-03 20:34:52.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.173][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-03 20:34:52.174][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-03 20:34:52.175][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-03 20:34:52.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.179][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-03 20:34:52.180][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-03 20:34:52.181][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-03 20:34:52.182][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-03 20:34:52.183][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-03 20:34:52.185][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-03 20:34:52.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.190][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-03 20:34:52.191][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-03 20:34:52.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.196][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-03 20:34:52.197][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-03 20:34:52.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.202][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-03 20:34:52.203][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-03 20:34:52.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.207][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-03 20:34:52.208][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-03 20:34:52.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.213][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-03 20:34:52.214][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-03 20:34:52.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.219][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-03 20:34:52.220][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-03 20:34:52.225][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-03 20:34:52.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.228][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[2025-02-03 20:34:52.229][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-03 20:34:52.231][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-03 20:34:52.232][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-03 20:34:52.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.240][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-03 20:34:52.278][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-03 20:34:52.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.297][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:52.298][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.300][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.302][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-03 20:34:52.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:52.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.305][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-03 20:34:52.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:52.306][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.307][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.308][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:52.308][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-03 20:34:52.308][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-03 20:34:52.308][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-03 20:34:52.308][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-03 20:34:52.309][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:52.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:52.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.321][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:52.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:52.324][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.325][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.326][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-03 20:34:52.328][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.329][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-03 20:34:52.330][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.331][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:52.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.332][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.333][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.334][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.335][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-03 20:34:52.336][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:52.337][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.338][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-03 20:34:52.339][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:52.340][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:52.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-03 20:34:52.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-03 20:34:52.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-03 20:34:52.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-03 20:34:52.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:52.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:52.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.349][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.350][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:52.351][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:52.352][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.353][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.354][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-03 20:34:52.355][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.356][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-03 20:34:52.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.358][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:52.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.360][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.361][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.362][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.363][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-03 20:34:52.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:52.365][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.366][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-03 20:34:52.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:52.368][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.369][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.369][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.370][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:52.371][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.373][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:52.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.377][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:52.378][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:52.379][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.380][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.381][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-03 20:34:52.383][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.384][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-03 20:34:52.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:52.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.390][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.391][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-03 20:34:52.392][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:52.393][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.394][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-03 20:34:52.395][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:52.396][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.397][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.398][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:52.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.401][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:52.402][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.404][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.405][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.406][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:52.407][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:52.408][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.409][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.413][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:52.413][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.494][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-03 20:34:52.503][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-03 20:34:52.505][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-03 20:34:52.506][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-03 20:34:52.508][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-03 20:34:52.509][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-03 20:34:52.510][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-03 20:34:52.511][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-03 20:34:52.513][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-03 20:34:52.514][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-03 20:34:52.515][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-03 20:34:52.517][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-03 20:34:52.518][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-03 20:34:52.519][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-03 20:34:52.520][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-03 20:34:52.522][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-03 20:34:52.523][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-03 20:34:52.524][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-03 20:34:52.525][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-03 20:34:52.527][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-03 20:34:52.528][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-03 20:34:52.529][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-03 20:34:52.531][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-03 20:34:52.532][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-03 20:34:52.533][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-03 20:34:52.535][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-03 20:34:52.536][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-03 20:34:52.537][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-03 20:34:52.539][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-03 20:34:52.540][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-03 20:34:52.541][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-03 20:34:52.542][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-03 20:34:52.544][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-03 20:34:52.545][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-03 20:34:52.546][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-03 20:34:52.548][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-03 20:34:52.549][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-03 20:34:52.550][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-03 20:34:52.551][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-03 20:34:52.553][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-03 20:34:52.554][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-03 20:34:52.556][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-03 20:34:52.557][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-03 20:34:52.558][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-03 20:34:52.561][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-03 20:34:52.562][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-03 20:34:52.563][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-03 20:34:52.565][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-03 20:34:52.566][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-03 20:34:52.567][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-03 20:34:52.569][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-03 20:34:52.570][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-03 20:34:52.571][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-03 20:34:52.573][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-03 20:34:52.574][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-03 20:34:52.575][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-03 20:34:52.577][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-03 20:34:52.578][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-03 20:34:52.579][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-03 20:34:52.581][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-03 20:34:52.582][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-03 20:34:52.583][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-03 20:34:52.585][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-03 20:34:52.586][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-03 20:34:52.588][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-03 20:34:52.589][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-03 20:34:52.590][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-03 20:34:52.592][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-03 20:34:52.593][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-03 20:34:52.595][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-03 20:34:52.596][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-03 20:34:52.597][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-03 20:34:52.599][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-03 20:34:52.600][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-03 20:34:52.602][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-03 20:34:52.603][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-03 20:34:52.605][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-03 20:34:52.606][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-03 20:34:52.608][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-03 20:34:52.609][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-03 20:34:52.611][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-03 20:34:52.612][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-03 20:34:52.614][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-03 20:34:52.620][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-03 20:34:52.622][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-03 20:34:52.625][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:52.626][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.628][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.639][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[2025-02-03 20:34:52.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.663][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[2025-02-03 20:34:52.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:52.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:52.776][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-03 20:34:52.786][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:52.789][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.790][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.792][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:52.793][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.794][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-03 20:34:52.795][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.797][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-03 20:34:52.798][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:52.799][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.800][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-03 20:34:52.801][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-03 20:34:52.802][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-03 20:34:52.804][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:52.805][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:52.805][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-03 20:34:52.805][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-03 20:34:52.806][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-03 20:34:52.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.809][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:52.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:52.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:52.812][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:52.813][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-03 20:34:52.813][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-03 20:34:52.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:52.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:52.816][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:52.817][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:52.823][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-03 20:34:52.825][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-03 20:34:52.827][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-03 20:34:52.828][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-03 20:34:52.830][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-03 20:34:52.853][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:52.854][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-03 20:34:52.859][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:52.863][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:52.868][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:52.869][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:52.870][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-03 20:34:52.871][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-02-03 20:34:52.872][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-03 20:34:52.872][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-02-03 20:34:52.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:52.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:52.875][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-02-03 20:34:52.876][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-02-03 20:34:52.877][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:52.902][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:52.904][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:52.905][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:52.906][private$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[2025-02-03 20:34:52.907][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:52.908][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-02-03 20:34:52.918][biodb::testThat]
biodb.INFO [2025-02-03 20:34:52.920][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-02-03 20:34:52.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:52.922][biodb::testThat]
biodb.TRACE[2025-02-03 20:34:52.929][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[2025-02-03 20:34:52.931][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:52.935][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:52.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:52.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:52.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:52.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:52.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:52.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:52.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-03 20:34:52.965][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:52.966][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:52.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:52.968][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:52.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:52.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:52.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:52.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:52.986][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:52.987][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:52.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:52.989][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.016][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.021][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.022][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.024][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.026][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.030][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.031][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.033][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.035][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.043][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.048][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.049][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.051][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.057][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.058][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.060][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.061][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.065][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.075][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.077][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.078][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.082][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.083][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.085][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.087][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.091][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.092][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.093][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.095][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.099][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.102][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.107][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:53.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:53.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.110][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:53.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:53.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.116][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.117][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.119][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.127][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.133][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.135][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.141][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.142][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.144][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:53.150][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:53.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.152][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.153][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:53.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:53.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.158][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:53.159][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.161][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.162][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:53.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.216][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.221][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.225][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.229][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.233][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.237][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:53.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.268][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.276][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:53.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.295][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.299][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.304][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.308][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.321][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:53.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:53.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:53.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:53.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:53.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:53.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.350][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.353][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.357][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.392][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.396][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.404][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.408][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:53.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:53.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.416][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:53.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:53.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:53.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:53.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.424][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:53.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:53.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:53.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.484][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.488][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.496][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:53.528][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-03 20:34:53.530][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-03 20:34:53.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-03 20:34:53.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-03 20:34:53.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-03 20:34:53.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-03 20:34:53.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-03 20:34:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-03 20:34:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-03 20:34:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.569][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.603][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.607][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.611][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:53.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.637][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.638][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.640][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.653][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.661][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.671][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.672][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.673][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.674][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.698][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.699][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.701][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.722][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.726][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.727][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.728][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.729][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:53.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.756][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:53.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.770][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.775][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.779][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.783][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.785][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.787][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.788][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:53.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.811][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.813][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:53.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.835][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.842][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.843][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.845][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.846][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:53.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:53.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.869][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.872][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:53.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:53.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.885][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.889][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.897][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.898][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.900][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.901][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:53.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.927][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.928][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.930][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:53.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.944][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.948][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.955][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.956][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.958][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:53.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.983][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.987][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.988][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.990][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:53.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:53.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:53.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.014][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.015][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.017][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.018][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.041][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.042][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.044][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.045][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.070][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.071][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.073][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.101][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.118][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.125][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.129][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.130][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.132][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.133][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.144][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.145][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.147][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.151][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.153][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.154][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.159][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.160][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.162][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.169][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.174][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.175][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.176][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.181][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.182][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.184][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.188][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.189][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.191][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.196][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.197][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.199][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.204][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.205][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.207][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.211][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:54.213][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:54.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.215][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.221][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.223][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.228][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.229][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.231][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.236][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.237][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.239][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.243][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.246][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.250][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.251][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.253][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.258][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.259][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.270][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.272][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.273][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.281][ef$get] fields variable is a list.
biodb.INFO [2025-02-03 20:34:54.288][biodb::testThat]
biodb.INFO [2025-02-03 20:34:54.289][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-03 20:34:54.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:54.291][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:54.305][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-03 20:34:54.312][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-03 20:34:54.317][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:54.319][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-03 20:34:54.321][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-02-03 20:34:54.322][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-03 20:34:54.324][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-02-03 20:34:54.325][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-03 20:34:54.350][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:54.351][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:54.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:54.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:54.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:54.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:54.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:54.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:54.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-03 20:34:54.367][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.368][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.370][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.376][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.377][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.379][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.381][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.385][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.386][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.388][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.389][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.393][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.394][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.396][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.397][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.404][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.414][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.415][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.417][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.422][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.423][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.425][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.426][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.430][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.431][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.433][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.435][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.438][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.439][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.441][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.446][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.447][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.449][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.451][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.455][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:54.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:54.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.457][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:54.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:54.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.463][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.464][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.465][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.471][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.472][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.474][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.479][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.480][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.482][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.488][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.491][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.497][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.498][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.500][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.507][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.509][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.511][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.515][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:54.516][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.519][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.520][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:54.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.537][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.541][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.545][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:54.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.549][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.552][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.562][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:54.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.592][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:54.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.600][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:54.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:54.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.624][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.632][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:54.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:54.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:54.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:54.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:54.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:54.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:54.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.714][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:54.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.725][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.729][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.733][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:54.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.741][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.744][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:54.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:54.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.748][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:54.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.764][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:54.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:54.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.791][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:54.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:54.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.806][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:54.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:54.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:54.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:54.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:54.834][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-03 20:34:54.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-03 20:34:54.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-03 20:34:54.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-03 20:34:54.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-03 20:34:54.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-03 20:34:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-03 20:34:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-03 20:34:54.858][biodb::testThat]
biodb.INFO [2025-02-03 20:34:54.859][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-03 20:34:54.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:54.861][biodb::testThat]
biodb.TRACE[2025-02-03 20:34:54.864][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.865][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.867][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:54.868][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-02-03 20:34:54.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:54.909][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-02-03 20:34:54.910][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-02-03 20:34:54.911][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-03 20:34:54.912][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-03 20:34:54.913][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:54.915][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:54.916][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:54.918][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:54.918][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:54.920][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:54.921][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:54.922][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:54.923][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:34:54.924][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:34:54.925][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-03 20:34:54.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:54.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:54.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:54.943][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:34:54.944][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:34:54.945][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-02-03 20:34:54.957][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.958][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.960][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:54.961][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-02-03 20:34:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:54.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:54.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:54.990][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[2025-02-03 20:34:55.041][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-03 20:34:55.043][private$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[2025-02-03 20:34:55.044][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-02-03 20:34:55.059][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.061][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.062][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:55.063][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.065][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:55.080][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:55.082][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:55.083][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:55.083][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:34:55.084][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:34:55.085][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-03 20:34:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:55.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:55.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.091][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:55.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.100][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:55.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:55.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.103][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:55.107][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:34:55.108][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:34:55.109][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-02-03 20:34:55.121][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.122][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.124][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:55.125][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-02-03 20:34:55.137][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:55.152][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-02-03 20:34:55.153][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-02-03 20:34:55.154][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-02-03 20:34:55.155][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-02-03 20:34:55.157][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.158][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.160][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:55.161][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.162][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:55.163][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:55.164][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:55.165][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:55.166][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:34:55.167][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:34:55.168][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-03 20:34:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.178][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:55.187][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:34:55.188][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:34:55.189][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-02-03 20:34:55.206][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.207][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-02-03 20:34:55.208][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:55.209][biodb::testThat]
biodb.TRACE[2025-02-03 20:34:55.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:55.244][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-02-03 20:34:55.245][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-03 20:34:55.246][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-02-03 20:34:55.254][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.255][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.257][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:55.258][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:55.259][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:55.260][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:55.261][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:55.262][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:55.263][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:34:55.264][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:34:55.265][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-03 20:34:55.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:55.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:55.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:55.282][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:34:55.283][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-02-03 20:34:55.298][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.299][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-02-03 20:34:55.300][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:55.301][biodb::testThat]
biodb.TRACE[2025-02-03 20:34:55.321][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.326][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.330][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-03 20:34:55.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-03 20:34:55.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.334][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-03 20:34:55.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-03 20:34:55.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.387][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-03 20:34:55.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-03 20:34:55.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-03 20:34:55.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:55.399][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-03 20:34:55.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-03 20:34:55.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:55.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-03 20:34:55.408][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.409][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-03 20:34:55.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:55.411][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.420][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.421][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-03 20:34:55.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:55.423][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.431][biodb::testThat]
biodb.INFO [2025-02-03 20:34:55.432][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-03 20:34:55.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:55.433][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:55.437][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-02-03 20:34:55.898][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-02-03 20:34:56.444][biodb::testThat]
biodb.INFO [2025-02-03 20:34:56.445][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-03 20:34:56.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:56.447][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:56.572][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-02-03 20:34:56.647][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:56.649][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:56.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:56.652][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:56.653][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:56.654][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:56.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:56.656][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:56.657][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:56.658][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:56.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:56.660][ef$get] fields variable is a list.
biodb.INFO [2025-02-03 20:34:56.662][biodb::testThat]
biodb.INFO [2025-02-03 20:34:56.663][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-02-03 20:34:56.664][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:56.665][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:56.667][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-02-03 20:34:56.975][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-03 20:34:56.977][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:56.978][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-03 20:34:56.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-02-03 20:34:56.998][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-03 20:34:56.999][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-03 20:34:57.000][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-03 20:34:57.002][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.003][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:57.005][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:57.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:57.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.017][FUN] Functions in observer BiodbConfig: [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[2025-02-03 20:34:57.019][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:57.053][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-02-03 20:34:57.054][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-02-03 20:34:57.073][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.074][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-02-03 20:34:57.075][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:57.077][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:57.085][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-02-03 20:34:57.086][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-02-03 20:34:57.087][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-03 20:34:57.089][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.091][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-03 20:34:57.093][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-02-03 20:34:57.095][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-03 20:34:57.096][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-03 20:34:57.097][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-03 20:34:57.099][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.100][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:57.102][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:57.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:57.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-03 20:34:57.117][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.122][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:57.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:57.157][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-02-03 20:34:57.158][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-02-03 20:34:57.159][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-02-03 20:34:57.175][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.176][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-02-03 20:34:57.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:57.178][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.207][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.209][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-02-03 20:34:57.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:57.211][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:57.215][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.217][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.218][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:57.220][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.221][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:57.223][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:57.224][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:57.225][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:57.226][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-02-03 20:34:57.235][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.236][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-02-03 20:34:57.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:57.238][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:57.241][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.243][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.245][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:57.246][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.247][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:57.249][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:57.250][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:57.251][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:57.252][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-02-03 20:34:57.262][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:57.264][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:57.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.267][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:57.268][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:57.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.270][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.271][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:57.273][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:57.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.275][ef$get] fields variable is a list.
biodb.INFO [2025-02-03 20:34:57.276][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-03 20:34:57.277][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-03 20:34:57.287][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-03 20:34:57.288][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-03 20:34:57.289][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.291][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.293][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.294][FUN] Functions in observer BiodbConfig: [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 [2025-02-03 20:34:57.298][biodb::testContext]
biodb.INFO [2025-02-03 20:34:57.299][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:57.300][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-02-03 20:34:57.301][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:57.302][biodb::testContext]
biodb.INFO [2025-02-03 20:34:57.306][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-03 20:34:57.308][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-03 20:34:57.312][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:57.313][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-03 20:34:57.315][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-03 20:34:57.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.319][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-03 20:34:57.320][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-03 20:34:57.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.324][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-03 20:34:57.325][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-03 20:34:57.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.329][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-03 20:34:57.330][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-03 20:34:57.331][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-03 20:34:57.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.336][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-03 20:34:57.337][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-03 20:34:57.338][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-03 20:34:57.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.342][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-03 20:34:57.343][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-03 20:34:57.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.347][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-03 20:34:57.348][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-03 20:34:57.349][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-03 20:34:57.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.353][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-03 20:34:57.354][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-03 20:34:57.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.357][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[2025-02-03 20:34:57.358][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-03 20:34:57.360][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-03 20:34:57.361][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-03 20:34:57.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.365][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-03 20:34:57.366][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-03 20:34:57.367][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-03 20:34:57.368][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-03 20:34:57.369][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-03 20:34:57.371][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-03 20:34:57.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.375][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-03 20:34:57.376][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-03 20:34:57.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.380][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-03 20:34:57.381][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-03 20:34:57.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.385][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-03 20:34:57.386][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-03 20:34:57.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.390][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-03 20:34:57.392][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-03 20:34:57.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.396][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-03 20:34:57.397][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-03 20:34:57.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.401][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-03 20:34:57.402][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-03 20:34:57.406][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-03 20:34:57.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.410][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-03 20:34:57.411][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-03 20:34:57.412][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-03 20:34:57.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.417][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-03 20:34:57.419][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.420][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-03 20:34:57.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:57.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.425][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.426][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.427][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.428][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-03 20:34:57.430][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:57.431][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.432][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-03 20:34:57.433][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:57.434][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.436][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.458][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:57.458][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-03 20:34:57.458][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-03 20:34:57.458][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-03 20:34:57.458][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-03 20:34:57.459][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:57.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.462][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:57.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.466][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.467][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:57.468][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:57.469][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.470][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.471][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-03 20:34:57.473][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.473][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-03 20:34:57.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:57.476][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.477][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.479][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.480][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-03 20:34:57.481][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:57.482][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.483][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-03 20:34:57.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:57.485][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.486][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.487][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:57.487][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-03 20:34:57.487][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-03 20:34:57.487][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-03 20:34:57.487][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-03 20:34:57.488][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:57.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:57.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.494][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.495][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:57.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:57.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.498][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.499][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-03 20:34:57.501][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.502][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-03 20:34:57.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:57.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.507][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.508][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.509][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-03 20:34:57.510][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:57.511][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.512][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-03 20:34:57.513][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:57.514][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.515][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.516][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.516][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:57.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.519][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:57.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.522][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.523][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.524][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:57.525][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:57.525][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.526][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.528][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-03 20:34:57.529][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.530][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-03 20:34:57.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:57.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.534][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.535][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.536][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.537][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-03 20:34:57.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:57.539][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.540][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-03 20:34:57.541][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:57.542][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.543][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.544][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:57.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.547][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:57.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.550][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.551][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.552][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:57.553][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:57.554][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.555][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.556][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:57.557][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.558][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[2025-02-03 20:34:57.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.562][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[2025-02-03 20:34:57.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.601][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[2025-02-03 20:34:57.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.606][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[2025-02-03 20:34:57.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.633][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-03 20:34:57.634][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-03 20:34:57.636][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-03 20:34:57.637][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-03 20:34:57.638][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-03 20:34:57.640][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-03 20:34:57.641][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-03 20:34:57.642][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-03 20:34:57.644][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-03 20:34:57.645][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-03 20:34:57.647][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-03 20:34:57.648][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-03 20:34:57.649][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-03 20:34:57.651][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-03 20:34:57.652][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-03 20:34:57.653][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-03 20:34:57.654][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-03 20:34:57.656][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-03 20:34:57.657][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-03 20:34:57.659][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-03 20:34:57.660][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-03 20:34:57.661][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-03 20:34:57.663][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-03 20:34:57.664][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-03 20:34:57.665][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-03 20:34:57.667][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-03 20:34:57.668][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-03 20:34:57.669][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-03 20:34:57.671][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-03 20:34:57.672][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-03 20:34:57.673][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-03 20:34:57.675][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-03 20:34:57.676][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-03 20:34:57.677][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-03 20:34:57.679][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-03 20:34:57.680][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-03 20:34:57.681][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-03 20:34:57.683][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-03 20:34:57.684][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-03 20:34:57.685][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-03 20:34:57.687][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-03 20:34:57.688][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-03 20:34:57.689][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-03 20:34:57.691][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-03 20:34:57.692][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-03 20:34:57.694][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-03 20:34:57.695][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-03 20:34:57.696][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-03 20:34:57.698][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-03 20:34:57.699][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-03 20:34:57.700][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-03 20:34:57.702][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-03 20:34:57.703][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-03 20:34:57.704][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-03 20:34:57.706][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-03 20:34:57.707][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-03 20:34:57.709][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-03 20:34:57.710][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-03 20:34:57.711][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-03 20:34:57.713][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-03 20:34:57.714][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-03 20:34:57.715][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-03 20:34:57.717][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-03 20:34:57.718][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-03 20:34:57.719][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-03 20:34:57.721][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-03 20:34:57.722][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-03 20:34:57.723][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-03 20:34:57.725][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-03 20:34:57.726][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-03 20:34:57.727][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-03 20:34:57.729][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-03 20:34:57.730][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-03 20:34:57.731][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-03 20:34:57.733][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-03 20:34:57.734][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-03 20:34:57.736][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-03 20:34:57.737][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-03 20:34:57.738][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-03 20:34:57.740][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-03 20:34:57.741][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-03 20:34:57.742][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-03 20:34:57.744][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-03 20:34:57.745][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-03 20:34:57.747][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-03 20:34:57.748][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:57.749][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.751][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.808][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[2025-02-03 20:34:57.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.814][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[2025-02-03 20:34:57.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.820][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[2025-02-03 20:34:57.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.826][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[2025-02-03 20:34:57.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.832][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[2025-02-03 20:34:57.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.839][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.DEBUG[2025-02-03 20:34:57.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.851][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[2025-02-03 20:34:57.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.857][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[2025-02-03 20:34:57.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:57.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:57.865][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-03 20:34:57.866][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:57.868][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.869][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.870][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.871][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:57.872][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.873][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-03 20:34:57.874][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.875][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.876][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-03 20:34:57.877][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:57.878][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.879][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-03 20:34:57.880][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-03 20:34:57.881][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-03 20:34:57.882][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:57.883][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:57.883][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-03 20:34:57.883][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-03 20:34:57.884][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-03 20:34:57.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.887][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:57.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:57.889][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:57.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:57.891][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-03 20:34:57.891][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-03 20:34:57.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:57.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:57.894][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:57.895][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:57.896][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-03 20:34:57.898][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-03 20:34:57.900][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-03 20:34:57.901][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-03 20:34:57.903][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-03 20:34:57.907][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:57.908][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-03 20:34:57.909][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:57.911][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:57.912][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:57.913][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:57.914][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-03 20:34:57.915][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-02-03 20:34:57.917][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-03 20:34:57.917][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-02-03 20:34:57.918][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:57.918][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:57.919][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-02-03 20:34:57.920][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-02-03 20:34:57.921][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:57.923][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:57.924][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:57.925][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:57.927][private$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[2025-02-03 20:34:57.928][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:57.929][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-02-03 20:34:57.930][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.931][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-02-03 20:34:57.932][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:57.933][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:57.937][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.939][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.940][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:57.942][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.943][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:57.944][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:57.945][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:57.946][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:57.947][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:34:57.950][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-02-03 20:34:57.956][biodb::testThat]
biodb.INFO [2025-02-03 20:34:57.957][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-02-03 20:34:57.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:57.959][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:57.961][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-02-03 20:34:57.962][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-03 20:34:57.963][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:57.965][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-03 20:34:57.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-02-03 20:34:57.968][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-03 20:34:57.970][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-02-03 20:34:57.971][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-03 20:34:57.973][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:57.974][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:57.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:57.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:57.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:57.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:57.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:57.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:57.984][FUN] Functions in observer BiodbConfig: [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[2025-02-03 20:34:57.988][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.991][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:57.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:57.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:57.996][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:57.997][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:57.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:57.999][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.000][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.005][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.006][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.008][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.009][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.013][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.014][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.016][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.018][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.022][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.023][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.025][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.031][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.032][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.034][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.041][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.043][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.045][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.047][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.051][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.052][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.054][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.055][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.059][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.060][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.062][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.068][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.069][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.071][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.077][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:58.078][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:58.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.080][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:58.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:58.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.085][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:58.086][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:58.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.088][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:58.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.093][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.094][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.096][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.102][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.103][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.104][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.110][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.113][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.118][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:58.119][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:58.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.121][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.122][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:58.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:58.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.126][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:58.127][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:58.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.129][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:58.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:58.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.135][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:58.136][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.138][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.139][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:58.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.155][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.158][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.162][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:58.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.170][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.174][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:58.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:58.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:58.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:58.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.213][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.221][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:58.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.225][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:58.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.237][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:58.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:58.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.241][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:58.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:58.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.244][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:58.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:58.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:58.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:58.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:58.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:58.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:58.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:58.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:58.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:58.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:58.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.295][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:58.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:58.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.326][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.333][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:58.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.345][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:58.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.349][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:58.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:58.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.352][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:58.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.356][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:58.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:58.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.360][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:58.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.376][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:58.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:58.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:58.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:58.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.400][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:58.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:58.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.404][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:58.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:58.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.412][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:58.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:58.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:58.439][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-02-03 20:34:58.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:58.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:58.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:58.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:58.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-03 20:34:58.457][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-03 20:34:58.458][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-03 20:34:58.459][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-03 20:34:58.460][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-03 20:34:58.461][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.463][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.464][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-03 20:34:58.469][biodb::testContext]
biodb.INFO [2025-02-03 20:34:58.470][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:58.471][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-02-03 20:34:58.472][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-03 20:34:58.473][biodb::testContext]
biodb.INFO [2025-02-03 20:34:58.476][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-03 20:34:58.478][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-03 20:34:58.482][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:58.483][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-03 20:34:58.484][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-03 20:34:58.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.487][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-03 20:34:58.488][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-03 20:34:58.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.492][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-03 20:34:58.493][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-03 20:34:58.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.495][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[2025-02-03 20:34:58.496][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-03 20:34:58.497][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-03 20:34:58.498][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-03 20:34:58.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.502][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-03 20:34:58.503][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-03 20:34:58.504][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-03 20:34:58.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.507][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-03 20:34:58.508][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-03 20:34:58.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.512][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-03 20:34:58.513][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-03 20:34:58.514][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-03 20:34:58.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.517][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-03 20:34:58.518][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-03 20:34:58.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.522][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-03 20:34:58.523][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-03 20:34:58.524][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-03 20:34:58.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.526][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[2025-02-03 20:34:58.527][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-03 20:34:58.528][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-03 20:34:58.529][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-03 20:34:58.530][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-03 20:34:58.531][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-03 20:34:58.532][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-03 20:34:58.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.535][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-03 20:34:58.536][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-03 20:34:58.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.539][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[2025-02-03 20:34:58.540][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-03 20:34:58.541][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-03 20:34:58.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.545][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-03 20:34:58.546][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-03 20:34:58.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.548][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[2025-02-03 20:34:58.549][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-03 20:34:58.550][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-03 20:34:58.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.554][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-03 20:34:58.555][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-03 20:34:58.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.557][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[2025-02-03 20:34:58.558][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-03 20:34:58.559][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-03 20:34:58.563][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-03 20:34:58.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.567][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-03 20:34:58.568][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-03 20:34:58.569][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-03 20:34:58.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.573][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-03 20:34:58.575][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.576][self$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[2025-02-03 20:34:58.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:58.579][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.581][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.582][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.583][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-03 20:34:58.584][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:58.585][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.586][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-03 20:34:58.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:58.588][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:58.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-03 20:34:58.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-03 20:34:58.590][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-03 20:34:58.590][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-03 20:34:58.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:58.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:58.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.596][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.597][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.598][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:58.599][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:58.600][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.601][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.602][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-03 20:34:58.604][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.605][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-03 20:34:58.606][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.607][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:58.608][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.609][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.610][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.611][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.612][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-03 20:34:58.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:58.614][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.615][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-03 20:34:58.615][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:58.616][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.617][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.618][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:58.618][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-03 20:34:58.618][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-03 20:34:58.618][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-03 20:34:58.618][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-03 20:34:58.619][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:58.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:58.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.625][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.626][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:58.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:58.629][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.630][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.631][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-03 20:34:58.632][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.633][self$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[2025-02-03 20:34:58.634][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.635][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:58.636][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.637][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.638][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.640][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-03 20:34:58.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:58.642][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.643][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-03 20:34:58.644][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:58.645][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.646][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.647][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.648][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:58.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.650][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:58.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.653][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.654][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.655][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:58.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:58.657][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.658][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.664][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-03 20:34:58.666][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.667][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-03 20:34:58.668][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.669][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:58.670][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.671][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.672][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.673][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-03 20:34:58.674][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:58.675][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.676][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-03 20:34:58.677][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:58.678][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.679][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.680][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.681][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-03 20:34:58.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:58.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:58.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:58.686][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.687][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.688][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:58.689][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:58.690][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.691][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:58.692][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:58.693][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.711][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[2025-02-03 20:34:58.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.729][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[2025-02-03 20:34:58.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.769][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-03 20:34:58.771][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-03 20:34:58.772][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-03 20:34:58.773][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-03 20:34:58.775][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-03 20:34:58.776][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-03 20:34:58.778][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-03 20:34:58.779][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-03 20:34:58.780][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-03 20:34:58.782][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-03 20:34:58.783][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-03 20:34:58.784][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-03 20:34:58.786][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-03 20:34:58.787][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-03 20:34:58.788][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-03 20:34:58.790][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-03 20:34:58.791][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-03 20:34:58.792][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-03 20:34:58.794][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-03 20:34:58.795][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-03 20:34:58.796][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-03 20:34:58.798][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-03 20:34:58.799][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-03 20:34:58.800][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-03 20:34:58.802][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-03 20:34:58.803][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-03 20:34:58.805][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-03 20:34:58.806][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-03 20:34:58.807][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-03 20:34:58.809][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-03 20:34:58.810][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-03 20:34:58.811][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-03 20:34:58.813][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-03 20:34:58.814][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-03 20:34:58.815][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-03 20:34:58.817][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-03 20:34:58.818][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-03 20:34:58.819][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-03 20:34:58.821][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-03 20:34:58.822][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-03 20:34:58.823][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-03 20:34:58.825][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-03 20:34:58.826][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-03 20:34:58.827][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-03 20:34:58.829][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-03 20:34:58.830][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-03 20:34:58.831][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-03 20:34:58.833][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-03 20:34:58.834][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-03 20:34:58.835][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-03 20:34:58.837][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-03 20:34:58.838][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-03 20:34:58.839][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-03 20:34:58.841][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-03 20:34:58.842][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-03 20:34:58.843][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-03 20:34:58.845][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-03 20:34:58.846][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-03 20:34:58.847][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-03 20:34:58.849][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-03 20:34:58.850][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-03 20:34:58.851][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-03 20:34:58.852][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-03 20:34:58.854][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-03 20:34:58.855][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-03 20:34:58.856][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-03 20:34:58.858][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-03 20:34:58.859][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-03 20:34:58.860][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-03 20:34:58.862][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-03 20:34:58.863][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-03 20:34:58.864][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-03 20:34:58.866][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-03 20:34:58.867][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-03 20:34:58.868][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-03 20:34:58.870][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-03 20:34:58.871][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-03 20:34:58.872][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-03 20:34:58.874][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-03 20:34:58.875][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-03 20:34:58.876][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-03 20:34:58.877][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-03 20:34:58.879][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-03 20:34:58.880][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-03 20:34:58.882][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-03 20:34:58.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-03 20:34:58.884][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.886][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.892][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[2025-02-03 20:34:58.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.922][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[2025-02-03 20:34:58.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.928][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[2025-02-03 20:34:58.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-03 20:34:58.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:58.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:58.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:58.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:58.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:58.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:58.989][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-03 20:34:58.990][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:58.992][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.993][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-03 20:34:58.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.995][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-03 20:34:58.996][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:58.997][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-03 20:34:58.998][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:58.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-03 20:34:59.000][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-03 20:34:59.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-03 20:34:59.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:59.003][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-03 20:34:59.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-03 20:34:59.005][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-03 20:34:59.006][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-03 20:34:59.007][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-03 20:34:59.007][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-03 20:34:59.007][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-03 20:34:59.008][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-03 20:34:59.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:59.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:59.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-03 20:34:59.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-03 20:34:59.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-03 20:34:59.013][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-03 20:34:59.014][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-03 20:34:59.014][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-03 20:34:59.015][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:59.016][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:59.017][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-03 20:34:59.018][self$setPropertyValue]
biodb.DEBUG[2025-02-03 20:34:59.019][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-03 20:34:59.020][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-03 20:34:59.022][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-03 20:34:59.023][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-03 20:34:59.025][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-03 20:34:59.028][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:59.029][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-03 20:34:59.030][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:59.031][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:59.032][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:59.033][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:59.034][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-03 20:34:59.041][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-02-03 20:34:59.042][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-03 20:34:59.042][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-02-03 20:34:59.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-03 20:34:59.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-03 20:34:59.045][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-02-03 20:34:59.045][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-02-03 20:34:59.046][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-03 20:34:59.048][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:59.049][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:59.050][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:59.051][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-03 20:34:59.052][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-03 20:34:59.053][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-02-03 20:34:59.054][biodb::testThat]
biodb.INFO [2025-02-03 20:34:59.055][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2025-02-03 20:34:59.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-03 20:34:59.057][biodb::testThat]
biodb.DEBUG[2025-02-03 20:34:59.059][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-03 20:34:59.060][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-02-03 20:34:59.061][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-02-03 20:34:59.064][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:59.065][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:59.066][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:34:59.068][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:59.069][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:34:59.070][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:34:59.071][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:34:59.072][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:34:59.073][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:34:59.074][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:34:59.074][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-02-03 20:34:59.076][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-03 20:34:59.077][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-03 20:34:59.079][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:59.080][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-03 20:34:59.082][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-02-03 20:34:59.083][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-03 20:34:59.085][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-02-03 20:34:59.086][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-03 20:34:59.087][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:59.088][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:59.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:59.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:59.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:59.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:59.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:59.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:59.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-03 20:34:59.102][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.105][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.110][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.111][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.113][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.114][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.118][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.119][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.121][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.122][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.126][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.127][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.129][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.130][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.134][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.135][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.137][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.142][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.143][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.145][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.150][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.151][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.153][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.154][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.158][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.159][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.161][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.167][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.168][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.169][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.175][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.176][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.177][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.183][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.186][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.187][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.191][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.192][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.194][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.202][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.207][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.208][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.211][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.217][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.218][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.220][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.225][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.226][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.228][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.230][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.234][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.235][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.237][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.243][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:59.244][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.246][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.248][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.269][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.273][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.277][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.281][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.284][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.323][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.338][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.345][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.353][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.360][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.391][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.395][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.398][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.429][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.442][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.446][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.457][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.465][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:59.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.480][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:59.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.504][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.508][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:59.543][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-03 20:34:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.548][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.552][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:34:59.559][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:34:59.560][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:34:59.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:59.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:59.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:59.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:59.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:59.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:59.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:34:59.571][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-02-03 20:34:59.572][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-03 20:34:59.574][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:34:59.575][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-02-03 20:34:59.578][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-02-03 20:34:59.579][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-03 20:34:59.580][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-02-03 20:34:59.581][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-02-03 20:34:59.582][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-03 20:34:59.584][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-03 20:34:59.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:34:59.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:34:59.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:34:59.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:34:59.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:34:59.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:34:59.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-03 20:34:59.598][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.599][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.600][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.606][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.607][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.609][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.610][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.614][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.615][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.617][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.622][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.623][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.625][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.626][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.630][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.631][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.633][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.638][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.639][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.641][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.647][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.648][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.650][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.655][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.656][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.658][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.659][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.663][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.664][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.665][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.671][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.672][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.673][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.679][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.679][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.681][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.686][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.689][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.694][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.695][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.697][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.702][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.703][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.705][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.711][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.713][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.718][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.719][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.721][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.722][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.729][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.734][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:59.735][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.737][ef$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.738][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-03 20:34:59.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:34:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:34:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.753][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.761][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-03 20:34:59.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.765][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.768][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-03 20:34:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-03 20:34:59.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-03 20:34:59.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.799][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-03 20:34:59.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.810][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-03 20:34:59.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.822][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-03 20:34:59.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.839][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.842][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.846][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:34:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:34:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-03 20:34:59.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-03 20:34:59.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-03 20:34:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-03 20:34:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.883][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.887][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-03 20:34:59.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-03 20:34:59.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.917][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.921][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.925][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-03 20:34:59.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.929][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.933][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.936][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-03 20:34:59.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.940][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.944][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-03 20:34:59.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-03 20:34:59.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.952][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:59.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.967][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-03 20:34:59.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-03 20:34:59.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-03 20:34:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-03 20:34:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.991][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:34:59.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:34:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:34:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.002][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:35:00.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-03 20:35:00.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-03 20:35:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-03 20:35:00.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:35:00.030][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-02-03 20:35:00.031][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.042][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:35:00.046][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:35:00.047][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:35:00.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:35:00.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:35:00.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:35:00.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:35:00.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:35:00.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:35:00.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:35:00.063][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-03 20:35:00.065][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-02-03 20:35:00.066][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-02-03 20:35:00.067][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:35:00.069][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:35:00.070][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:35:00.072][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:35:00.073][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:35:00.074][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:35:00.075][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:35:00.076][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:35:00.077][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:35:00.078][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:35:00.079][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-03 20:35:00.080][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.084][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.092][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.099][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.103][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:35:00.107][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:35:00.108][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:35:00.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:35:00.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:35:00.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:35:00.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:35:00.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:35:00.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:35:00.117][FUN] Functions in observer BiodbConfig: [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[2025-02-03 20:35:00.119][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.122][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.134][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.141][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:35:00.145][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-02-03 20:35:00.146][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:35:00.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:35:00.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:35:00.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:35:00.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:35:00.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:35:00.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:35:00.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-03 20:35:00.161][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-02-03 20:35:00.162][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-02-03 20:35:00.163][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-02-03 20:35:00.165][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:35:00.166][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:35:00.168][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-02-03 20:35:00.169][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-02-03 20:35:00.170][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-02-03 20:35:00.171][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-02-03 20:35:00.172][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-02-03 20:35:00.173][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-02-03 20:35:00.174][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-02-03 20:35:00.175][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-02-03 20:35:00.176][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-02-03 20:35:00.177][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.181][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.185][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.196][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.200][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:35:00.204][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-02-03 20:35:00.205][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-02-03 20:35:00.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:35:00.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:35:00.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:35:00.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:35:00.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:35:00.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:35:00.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-03 20:35:00.221][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.225][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.229][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.233][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.240][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-03 20:35:00.244][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-03 20:35:00.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-03 20:35:00.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-03 20:35:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-03 20:35:00.248][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-02-03 20:35:00.249][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-02-03 20:35:00.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-03 20:35:00.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:35:00.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:35:00.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:35:00.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:35:00.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:35:00.258][FUN] Functions in observer BiodbConfig: [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 [2025-02-03 20:35:00.265][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-03 20:35:00.266][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-03 20:35:00.267][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-03 20:35:00.268][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-03 20:35:00.269][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-03 20:35:00.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-03 20:35:00.270][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-03 20:35:00.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-03 20:35:00.272][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-03 20:35:00.273][FUN] Functions in observer 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 2 | WARN 0 | SKIP 0 | PASS 241 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:19:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE
`actual`:
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.na(content))
── Failure ('test_100_generic.R:19:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE
`actual`:
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─testthat::expect_true(nchar(content) > 0)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 241 ]
Error: Test failures
Execution halted