Pierrick Roger
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/biodbHmdb |
| git_branch: RELEASE_3_19 |
| git_last_commit: 86c2780 |
| git_last_commit_date: 2024-09-30 04:28:41 -0400 (Mon, 30 Sep 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbHmdb 1.10.2 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.10.2 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbHmdb_1.10.2.tar.gz |
| StartedAt: 2024-10-16 22:08:27 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 22:09:23 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 56.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbHmdb_1.10.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.10.2’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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 ... ERROR
Running examples in ‘biodbHmdb-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmdbToSqlite
> ### Title: Convert HMDB Metabolites to a SQLite database.
> ### Aliases: hmdbToSqlite
>
> ### ** Examples
>
> # Copy all HMDB entries into a new SQLite database:
> biodbHmdb::hmdbToSqlite('myfile.sqlite')
INFO [22:09:07.681] Loading definitions from package biodb version 1.12.0.
INFO [22:09:07.825] Loading definitions from package biodbHmdb version 1.10.2.
Loading required package: biodb
INFO [22:09:07.925] Extract whole database of hmdb.metabolites.
INFO [22:09:07.927] Extracting content of downloaded',
' HMDB metabolite database...
Warning in normalizePath(zipfile) :
path[1]="/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip": No such file or directory
Error in zip::unzip(zip.path, exdir = extract.dir) :
zip error: Cannot open zip file `/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip` for reading in file zip.c:137
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbHmdb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘biodbHmdb’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c EntryMaker.cpp -o EntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c FileEntryMaker.cpp -o FileEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c TagDetector.cpp -o TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c XmlSplitter.cpp -o XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-TagDetector.cpp -o test-100-TagDetector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-biodbHmdb/00new/biodbHmdb/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-10-16 22:09:10.484][biodb::testContext]
biodb.INFO [2024-10-16 22:09:10.487][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:10.488][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2024-10-16 22:09:10.488][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:10.489][biodb::testContext]
biodb.INFO [2024-10-16 22:09:10.491][biodb::testThat]
biodb.INFO [2024-10-16 22:09:10.492][biodb::testThat] Running test function test_extractXmlEntries (" extractXmlEntries() works fine. ").
biodb.INFO [2024-10-16 22:09:10.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:10.494][biodb::testThat]
biodb.INFO [2024-10-16 22:09:10.601][biodb::testContext]
biodb.INFO [2024-10-16 22:09:10.603][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:10.604][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-16 22:09:10.605][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:10.606][biodb::testContext]
biodb.INFO [2024-10-16 22:09:10.615][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:10.630][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:10.639][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:10.640][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:10.641][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:10.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.645][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:10.666][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:10.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.671][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:10.673][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:10.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.677][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:10.678][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:10.679][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:10.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.683][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:10.684][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:10.685][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:10.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.689][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:10.690][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:10.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.694][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:10.695][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:10.696][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:10.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.699][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:10.701][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:10.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.704][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:10.705][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:10.706][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:10.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.710][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:10.711][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:10.712][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:10.713][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:10.714][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:10.715][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:10.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.719][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:10.720][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:10.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.724][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:10.725][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:10.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.729][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:10.730][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:10.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.734][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:10.735][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:10.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.738][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[2024-10-16 22:09:10.739][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:10.740][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:10.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.744][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:10.745][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:10.749][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:10.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.751][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[2024-10-16 22:09:10.752][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:10.753][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:10.754][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:10.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.761][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:10.796][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.812][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:10.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:10.822][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.823][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.824][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.825][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:10.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:10.827][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.828][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:10.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:10.830][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.831][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.832][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:10.832][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:10.832][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:10.832][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:10.832][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:10.833][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:10.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.836][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:10.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.839][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.840][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.841][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:10.842][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:10.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.843][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.845][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:10.847][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.848][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:10.848][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.850][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:10.851][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.852][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.852][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.853][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.854][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:10.855][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:10.856][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.857][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:10.858][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:10.859][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.860][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.861][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:10.861][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:10.861][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:10.861][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:10.861][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:10.862][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:10.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:10.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.868][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:10.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:10.871][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.872][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.874][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:10.875][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.877][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:10.878][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.879][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:10.880][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.881][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.883][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.884][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.884][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:10.885][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:10.886][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.887][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:10.888][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:10.889][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.890][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.891][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.892][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:10.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.895][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:10.896][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.897][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.897][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.898][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.899][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:10.900][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:10.901][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.902][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.903][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:10.905][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.906][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:10.907][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.908][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:10.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.910][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.911][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.912][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:10.913][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:10.914][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.915][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:10.916][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:10.917][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.918][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:10.919][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.920][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:10.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.922][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:10.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:10.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:10.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:10.926][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.927][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:10.928][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:10.929][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:10.929][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:10.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:10.934][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.952][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[2024-10-16 22:09:10.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.969][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[2024-10-16 22:09:10.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:10.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.017][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:11.022][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:11.023][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:11.024][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:11.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:11.027][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:11.029][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:11.030][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:11.032][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:11.033][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:11.034][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:11.036][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:11.037][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:11.039][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:11.040][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:11.041][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:11.043][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:11.044][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:11.046][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:11.047][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:11.048][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:11.050][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:11.051][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:11.053][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:11.054][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:11.055][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:11.057][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:11.058][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:11.060][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:11.061][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:11.062][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:11.064][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:11.065][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:11.067][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:11.068][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:11.069][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:11.071][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:11.072][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:11.074][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:11.075][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:11.076][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:11.078][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:11.079][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:11.080][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:11.082][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:11.083][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:11.085][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:11.086][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:11.088][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:11.090][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:11.091][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:11.093][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:11.095][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:11.096][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:11.097][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:11.099][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:11.100][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:11.101][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:11.103][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:11.104][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:11.105][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:11.107][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:11.108][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:11.109][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:11.111][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:11.112][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:11.113][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:11.115][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:11.116][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:11.117][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:11.119][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:11.120][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:11.121][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:11.122][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:11.124][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:11.125][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:11.126][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:11.128][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:11.129][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:11.130][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:11.132][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:11.133][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:11.134][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:11.140][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:11.142][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:11.145][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:11.146][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.148][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.195][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[2024-10-16 22:09:11.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.262][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:11.271][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:11.273][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.274][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.275][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:11.277][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.278][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-16 22:09:11.279][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.280][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.281][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:09:11.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:11.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.284][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-16 22:09:11.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-16 22:09:11.286][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-16 22:09:11.287][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.288][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:11.288][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-16 22:09:11.288][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-16 22:09:11.289][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:09:11.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.292][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:11.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.295][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-16 22:09:11.295][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-16 22:09:11.296][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:11.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:11.298][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.299][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.307][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-16 22:09:11.309][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:11.311][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:11.312][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:11.313][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:11.336][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:11.338][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-16 22:09:11.376][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:11.381][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:11.385][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:11.386][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:11.388][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-16 22:09:11.389][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-16 22:09:11.390][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-16 22:09:11.390][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-16 22:09:11.391][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:11.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:11.392][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-16 22:09:11.393][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-16 22:09:11.394][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:11.413][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:11.415][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:11.416][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:11.417][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:11.418][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:11.419][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-16 22:09:11.421][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:09:11.422][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-16 22:09:11.430][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-16 22:09:11.431][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:09:11.431][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.433][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.435][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:11.439][biodb::testContext]
biodb.INFO [2024-10-16 22:09:11.440][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:11.441][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2024-10-16 22:09:11.442][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:11.443][biodb::testContext]
biodb.INFO [2024-10-16 22:09:11.446][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:11.448][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:11.452][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:11.453][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:11.454][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:11.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.457][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:11.458][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:11.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.462][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:11.463][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:11.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.466][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:11.467][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:11.468][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:11.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.471][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[2024-10-16 22:09:11.471][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:11.472][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:11.473][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:11.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.477][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:11.478][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:11.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.482][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:11.483][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:11.484][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:11.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.487][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:11.488][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:11.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.491][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[2024-10-16 22:09:11.491][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:11.492][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:11.493][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:11.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.497][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:11.498][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:11.499][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:11.500][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:11.501][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:11.502][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:11.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.506][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:11.507][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:11.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.510][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:11.511][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:11.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.515][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:11.516][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:11.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.519][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:11.520][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:11.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.524][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:11.525][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:11.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.528][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:11.529][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:11.532][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:11.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.541][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:11.542][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:11.543][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:11.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.546][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:11.548][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.549][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:11.550][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:11.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.554][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.555][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.556][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:11.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:11.558][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.559][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:11.560][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:11.561][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.562][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.563][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:11.563][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:11.563][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:11.563][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:11.563][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:11.564][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:11.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:11.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.570][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:11.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:11.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.573][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.575][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:11.576][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.577][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:11.578][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:11.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.584][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:11.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:11.586][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.587][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:11.588][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:11.589][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.590][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.591][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:11.591][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:11.591][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:11.591][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:11.591][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:11.592][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:11.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:11.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.598][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:11.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:11.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.602][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.603][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:11.605][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.607][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:11.608][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:11.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.615][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:11.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:11.617][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.618][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:11.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:11.620][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.621][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:11.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:11.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.629][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:11.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:11.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.632][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.633][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:11.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:11.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.638][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:11.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.641][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.642][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.643][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:11.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:11.645][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.646][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:11.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:11.648][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.648][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.649][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:11.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:11.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:11.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:11.656][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.657][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:11.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:11.661][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.662][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:11.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:11.665][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.698][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[2024-10-16 22:09:11.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.702][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[2024-10-16 22:09:11.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.707][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[2024-10-16 22:09:11.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.726][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[2024-10-16 22:09:11.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.748][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:11.749][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:11.751][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:11.752][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:11.753][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:11.755][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:11.756][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:11.758][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:11.759][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:11.760][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:11.762][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:11.763][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:11.764][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:11.765][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:11.767][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:11.768][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:11.769][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:11.771][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:11.772][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:11.773][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:11.775][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:11.776][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:11.777][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:11.779][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:11.780][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:11.781][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:11.783][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:11.784][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:11.786][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:11.787][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:11.788][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:11.790][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:11.791][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:11.793][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:11.794][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:11.795][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:11.797][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:11.798][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:11.799][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:11.801][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:11.802][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:11.803][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:11.805][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:11.807][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:11.808][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:11.810][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:11.812][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:11.813][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:11.815][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:11.817][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:11.818][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:11.819][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:11.821][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:11.822][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:11.823][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:11.825][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:11.826][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:11.827][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:11.829][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:11.830][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:11.831][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:11.833][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:11.834][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:11.835][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:11.837][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:11.838][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:11.839][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:11.841][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:11.842][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:11.848][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:11.849][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:11.850][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:11.852][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:11.853][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:11.854][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:11.856][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:11.857][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:11.858][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:11.859][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:11.861][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:11.862][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:11.863][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:11.865][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:11.866][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:11.868][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:11.869][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:11.870][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.871][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.898][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[2024-10-16 22:09:11.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:11.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.979][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:11.981][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:11.982][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.983][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.984][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:11.987][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:11.988][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-16 22:09:11.989][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:11.990][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:09:11.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:11.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:11.993][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-16 22:09:11.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-16 22:09:12.000][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-16 22:09:12.001][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:12.002][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:12.002][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-16 22:09:12.002][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-16 22:09:12.003][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:09:12.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:12.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:12.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:12.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:12.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:12.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:12.009][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-16 22:09:12.009][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-16 22:09:12.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:12.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:12.012][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:12.013][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:12.015][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-16 22:09:12.016][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:12.018][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:12.020][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:12.022][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:12.025][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:12.026][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-16 22:09:12.027][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:12.029][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:12.030][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:12.031][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:12.032][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-16 22:09:12.033][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-16 22:09:12.034][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-16 22:09:12.034][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-16 22:09:12.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:12.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:12.037][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-16 22:09:12.038][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-16 22:09:12.039][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:12.040][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:12.041][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:12.042][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:12.044][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:12.045][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:12.046][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-16 22:09:12.047][biodb::testThat]
biodb.INFO [2024-10-16 22:09:12.048][biodb::testThat] Running test function test.hmdbmetabolite.nbentries (" HMDB metabolite returns enough entries. ").
biodb.INFO [2024-10-16 22:09:12.049][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:12.050][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:12.061][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-10-16 22:09:12.063][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-10-16 22:09:12.064][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-10-16 22:09:12.066][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-10-16 22:09:12.067][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-10-16 22:09:12.069][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:12.070][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-10-16 22:09:12.071][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-10-16 22:09:12.073][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker173e4424fbabdcmarker".
biodb.TRACE[2024-10-16 22:09:12.075][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-10-16 22:09:12.076][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:12.077][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-10-16 22:09:12.079][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-10-16 22:09:12.080][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2024-10-16 22:09:12.081][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-10-16 22:09:12.082][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2024-10-16 22:09:12.086][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-10-16 22:09:12.087][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-10-16 22:09:12.088][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-10-16 22:09:12.959][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2024-10-16 22:09:12.968][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-10-16 22:09:12.970][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-16 22:09:12.971][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:12.972][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-10-16 22:09:12.974][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker173e4478c175d0marker".
biodb.TRACE[2024-10-16 22:09:12.976][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-10-16 22:09:12.977][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:12.978][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-16 22:09:12.979][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:12.980][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-16 22:09:12.982][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-16 22:09:12.991][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-16 22:09:12.993][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-16 22:09:12.994][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-16 22:09:12.997][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-10-16 22:09:13.003][biodb::testThat]
biodb.INFO [2024-10-16 22:09:13.004][biodb::testThat] Running test function test.old.accession (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2024-10-16 22:09:13.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:13.006][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:13.021][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-10-16 22:09:13.023][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-16 22:09:13.024][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:13.026][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-16 22:09:13.028][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-10-16 22:09:13.029][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:13.031][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-16 22:09:13.032][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:13.034][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:13.038][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-16 22:09:13.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:13.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:13.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:13.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.058][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.TRACE[2024-10-16 22:09:13.080][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.081][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.101][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.103][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.104][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.132][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.136][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.138][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.139][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.141][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.145][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.146][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.148][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.150][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.157][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.163][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.164][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.165][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.171][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.172][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.174][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.180][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.181][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.183][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.184][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.188][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.189][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.191][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.197][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.198][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.200][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.206][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.207][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.209][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.210][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.224][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.238][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.239][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.241][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.246][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.247][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.249][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.255][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:13.256][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:13.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.258][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.259][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:13.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:13.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.264][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.266][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.268][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.272][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-16 22:09:13.273][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.275][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.276][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-16 22:09:13.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.327][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.332][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.336][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:13.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.340][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.345][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.349][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:13.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.390][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:13.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:13.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.406][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.410][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:13.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.418][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:13.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:13.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.422][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:13.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:13.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.426][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:13.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:13.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.438][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.466][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.470][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.474][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.509][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.512][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.516][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:13.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.521][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.525][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.529][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:13.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-16 22:09:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-16 22:09:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.605][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:13.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:13.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.609][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:13.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:13.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:13.653][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-10-16 22:09:13.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:13.673][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:09:13.674][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-16 22:09:13.675][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-16 22:09:13.676][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:09:13.677][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:13.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:13.679][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.681][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:13.686][biodb::testContext]
biodb.INFO [2024-10-16 22:09:13.687][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:13.688][biodb::testContext] Test context - Test search of entries
biodb.INFO [2024-10-16 22:09:13.689][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:13.690][biodb::testContext]
biodb.INFO [2024-10-16 22:09:13.694][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:13.696][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:13.700][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:13.701][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:13.702][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:13.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.706][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:13.707][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:13.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.711][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:13.712][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:13.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.716][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:13.717][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:13.718][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:13.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.722][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:13.723][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:13.724][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:13.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.728][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:13.729][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:13.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.733][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:13.734][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:13.735][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:13.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.738][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[2024-10-16 22:09:13.739][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:13.740][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:13.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.744][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:13.745][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:13.746][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:13.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.749][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:13.750][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:13.751][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:13.753][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:13.754][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:13.755][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:13.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.758][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:13.759][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:13.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.763][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:13.764][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:13.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.768][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:13.769][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:13.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.772][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:13.773][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:13.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.777][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:13.778][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:13.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.782][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:13.783][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:13.786][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:13.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.796][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:13.797][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:13.798][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:13.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.802][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:13.803][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.804][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:13.805][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.806][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:13.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.811][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:13.812][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:13.813][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.814][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:13.815][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:13.816][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.817][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.818][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:13.818][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:13.818][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:13.818][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:13.818][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:13.819][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:13.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.822][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:13.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.825][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.826][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.827][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:13.828][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:13.829][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.830][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.831][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:13.833][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.834][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:13.835][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:13.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.838][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.839][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.840][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.841][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:13.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:13.843][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.844][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:13.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:13.846][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.848][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:13.848][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:13.848][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:13.848][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:13.848][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:13.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:13.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:13.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.856][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:13.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:13.858][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.859][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.861][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:13.862][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.864][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:13.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:13.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.868][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.870][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:13.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:13.873][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.874][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:13.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:13.875][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.877][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.878][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:13.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:13.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.885][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.886][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:13.887][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:13.888][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.889][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.890][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:13.892][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.893][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:13.894][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:13.896][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.897][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.898][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.899][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.900][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:13.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:13.902][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.903][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:13.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:13.905][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.906][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:13.907][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:13.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:13.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:13.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:13.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:13.915][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:13.917][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:13.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:13.919][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:13.920][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:13.921][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.963][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[2024-10-16 22:09:13.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.981][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[2024-10-16 22:09:13.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:13.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:13.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.005][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:14.007][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:14.008][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:14.010][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:14.011][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:14.013][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:14.014][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:14.016][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:14.017][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:14.018][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:14.020][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:14.021][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:14.023][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:14.024][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:14.026][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:14.027][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:14.028][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:14.030][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:14.031][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:14.033][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:14.034][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:14.036][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:14.037][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:14.038][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:14.040][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:14.041][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:14.043][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:14.044][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:14.046][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:14.047][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:14.049][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:14.050][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:14.051][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:14.053][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:14.054][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:14.056][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:14.057][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:14.059][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:14.060][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:14.061][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:14.063][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:14.064][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:14.072][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:14.073][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:14.075][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:14.076][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:14.077][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:14.079][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:14.080][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:14.082][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:14.083][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:14.084][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:14.086][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:14.087][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:14.088][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:14.090][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:14.091][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:14.093][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:14.094][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:14.096][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:14.097][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:14.098][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:14.100][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:14.101][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:14.103][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:14.104][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:14.105][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:14.107][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:14.108][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:14.110][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:14.111][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:14.112][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:14.114][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:14.115][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:14.117][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:14.118][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:14.119][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:14.121][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:14.122][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:14.124][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:14.125][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:14.127][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:14.128][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:14.129][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:14.131][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:14.132][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:14.133][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.135][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.212][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[2024-10-16 22:09:14.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.218][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[2024-10-16 22:09:14.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:14.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.252][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:14.253][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:14.255][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:14.256][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:14.257][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:14.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:14.259][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:14.260][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-16 22:09:14.261][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:14.262][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:14.263][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:09:14.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:14.265][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:14.266][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-16 22:09:14.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-16 22:09:14.268][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-16 22:09:14.270][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:14.271][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:14.271][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-16 22:09:14.271][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-16 22:09:14.272][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:09:14.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:14.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:14.275][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:14.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:14.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:14.277][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:14.278][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-16 22:09:14.278][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-16 22:09:14.280][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:14.280][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:14.281][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:14.282][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:14.284][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-16 22:09:14.285][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:14.287][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:14.289][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:14.290][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:14.294][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:14.295][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-16 22:09:14.296][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:14.297][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:14.299][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:14.300][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:14.301][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-16 22:09:14.302][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-16 22:09:14.303][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-16 22:09:14.303][self$setPropertyValue] Setting property "urls" to "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-16 22:09:14.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:14.305][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:14.306][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-16 22:09:14.307][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-16 22:09:14.308][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-16 22:09:14.309][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:14.311][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:14.312][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:14.313][private$addConnectorRules] Create new rule for URL "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-16 22:09:14.314][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:14.315][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-16 22:09:14.317][biodb::testThat]
biodb.INFO [2024-10-16 22:09:14.318][biodb::testThat] Running test function test.searchMultipleWordsInDescription (" We can search for multiple words inside description field. ").
biodb.INFO [2024-10-16 22:09:14.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:14.320][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:14.322][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-16 22:09:14.323][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-10-16 22:09:14.324][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-10-16 22:09:14.327][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:14.329][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:14.330][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-16 22:09:14.331][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:14.332][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-16 22:09:14.334][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-16 22:09:14.343][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-16 22:09:14.344][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-16 22:09:14.345][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-16 22:09:14.346][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-10-16 22:09:14.347][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2024-10-16 22:09:14.349][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-10-16 22:09:14.350][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-16 22:09:14.352][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:14.353][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-16 22:09:14.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-10-16 22:09:14.357][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:14.365][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-10-16 22:09:14.366][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:14.367][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:14.368][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-16 22:09:14.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:14.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:14.383][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.386][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.392][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.393][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.395][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.400][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.401][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.403][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.405][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.409][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.410][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.412][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.413][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.417][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.420][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.426][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.427][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.438][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.439][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.443][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.444][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.446][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.448][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.452][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.453][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.455][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.456][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.461][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.462][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.464][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.469][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:14.470][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:14.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.472][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:14.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.478][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:14.479][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:14.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.481][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:14.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.486][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.487][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.489][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.495][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.496][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.498][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.504][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.505][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.513][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.519][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.520][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.522][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.523][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.527][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:14.528][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:14.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.530][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.536][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-16 22:09:14.537][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.539][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.540][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-16 22:09:14.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.561][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.565][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:14.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.569][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.573][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.577][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:14.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.634][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.638][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.646][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.651][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.655][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.678][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.682][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:14.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:14.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:14.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:14.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:14.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:14.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:14.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:14.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:14.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:14.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.715][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.719][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.723][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.727][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:14.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.755][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.763][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:14.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.767][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.771][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.775][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:14.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:14.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:14.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.782][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:14.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-16 22:09:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.804][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-16 22:09:14.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:14.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.824][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:14.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:14.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.831][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.835][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.842][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:14.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:14.868][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-10-16 22:09:14.869][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.873][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.877][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:14.880][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:14.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:14.884][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-16 22:09:14.885][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-16 22:09:14.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:14.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.909][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-10-16 22:09:14.956][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-16 22:09:14.958][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:14.960][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-16 22:09:14.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-10-16 22:09:14.976][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:14.977][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-16 22:09:14.979][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:15.001][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:15.002][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-16 22:09:15.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:15.015][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.018][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.023][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.024][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.026][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.027][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.031][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.032][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.034][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.035][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.043][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.044][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.046][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.047][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.051][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.052][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.053][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.058][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.059][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.061][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.066][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.067][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.069][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.070][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.074][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.075][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.077][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.081][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.082][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.084][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.089][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.090][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.092][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.097][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.098][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.100][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.101][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.104][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.105][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.107][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.112][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.113][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.115][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.121][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.122][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.127][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.130][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.135][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.136][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.138][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.139][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.143][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:15.144][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:15.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.146][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.147][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:15.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:15.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.151][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-16 22:09:15.152][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.153][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.154][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-16 22:09:15.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.174][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.178][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.181][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:15.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.185][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.189][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.192][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-16 22:09:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:15.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-16 22:09:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:15.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.229][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-16 22:09:15.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-16 22:09:15.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.255][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.270][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.316][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.320][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.323][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.346][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.349][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.353][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.357][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:15.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.360][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-16 22:09:15.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:15.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:15.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:15.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:15.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.379][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:15.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:15.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.382][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-16 22:09:15.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-16 22:09:15.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:15.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:15.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.421][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.424][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:15.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:15.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.432][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:15.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:15.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:15.464][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-10-16 22:09:15.473][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.477][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.480][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.484][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:15.488][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-16 22:09:15.489][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2024-10-16 22:09:15.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:15.551][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-16 22:09:15.553][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-10-16 22:09:15.553][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.INFO [2024-10-16 22:09:15.571][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-10-16 22:09:15.573][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-10-16 22:09:15.574][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-10-16 22:09:15.575][private$doDownload] Downloading HMDB metabolite database at "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2024-10-16 22:09:15.576][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2024-10-16 22:09:15.577][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-10-16 22:09:15.579][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:15.580][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-10-16 22:09:15.581][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-10-16 22:09:15.583][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker173e447581aef4marker".
biodb.TRACE[2024-10-16 22:09:15.584][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-10-16 22:09:15.585][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:15.586][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-10-16 22:09:15.587][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-10-16 22:09:15.588][private$doExtractDownload] Extracting content of downloaded',
' HMDB metabolite database...
biodb.DEBUG[2024-10-16 22:09:15.589][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-10-16 22:09:15.590][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2024-10-16 22:09:15.593][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-10-16 22:09:15.594][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2024-10-16 22:09:15.595][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-10-16 22:09:15.596][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_two_full_entries.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2024-10-16 22:09:15.604][self$addFilesToCache] Moving files to cache [2]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2024-10-16 22:09:15.605][private$doAddFilesToCache] Destination files are [2]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-16 22:09:15.606][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:15.607][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-10-16 22:09:15.608][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker173e44eb7aacfmarker".
biodb.TRACE[2024-10-16 22:09:15.610][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-10-16 22:09:15.610][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-10-16 22:09:15.611][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-16 22:09:15.613][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:15.614][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-16 22:09:15.628][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-16 22:09:15.629][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-16 22:09:15.630][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-16 22:09:15.631][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-16 22:09:15.632][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-10-16 22:09:15.633][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-10-16 22:09:15.635][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.639][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.642][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.646][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.650][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.654][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.657][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:15.661][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-16 22:09:15.662][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-16 22:09:15.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.676][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.680][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.684][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.687][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.700][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:15.703][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-10-16 22:09:15.704][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-16 22:09:15.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.714][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[2024-10-16 22:09:15.718][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-16 22:09:15.719][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-10-16 22:09:15.720][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-10-16 22:09:15.722][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:15.723][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:15.725][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-16 22:09:15.726][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-16 22:09:15.727][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-16 22:09:15.728][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-16 22:09:15.729][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-16 22:09:15.730][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-16 22:09:15.731][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-16 22:09:15.732][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-10-16 22:09:15.733][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-10-16 22:09:15.734][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.742][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.746][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.749][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.753][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.757][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:15.761][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-10-16 22:09:15.761][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2024-10-16 22:09:15.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.776][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.779][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.783][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.791][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-16 22:09:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-16 22:09:15.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:15.798][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-16 22:09:15.799][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-16 22:09:15.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:15.815][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:09:15.816][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-16 22:09:15.817][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-16 22:09:15.818][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:09:15.819][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.821][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.822][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
>
> proc.time()
user system elapsed
6.180 1.096 7.347
biodbHmdb.Rcheck/biodbHmdb-Ex.timings
| name | user | system | elapsed | |
| HmdbMetabolitesConn | 0.488 | 0.047 | 0.536 | |
| HmdbMetabolitesEntry | 0.112 | 0.000 | 0.112 | |